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/7916125/working'
mkdir: created directory `/scratch/stefan/7916125/working/protonate'
Storing results in /scratch/stefan/7916125/finished
Working in /scratch/stefan/7916125/working
/scratch/stefan/7916125/working /scratch/stefan/7916125

/scratch/stefan/7916125/working/protonate /scratch/stefan/7916125/working /scratch/stefan/7916125
Precomputing protomers for all compounds (pH: 7.4)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
ph 7.4: 1032 protomers created
Coalesing and merging protomers
1010 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1012 protomers after new stereo-center expansion
/scratch/stefan/7916125/working /scratch/stefan/7916125

Bulk generating 3D conformations all protomers in /scratch/stefan/7916125/working/3D
mkdir: created directory `/scratch/stefan/7916125/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7916125/working/protonate/xaaaaaf-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'
1013 3D conformations generated for 1000 compounds

Building REAL250005042893
mkdir: created directory `/scratch/stefan/7916125/working/building'
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042893'
/scratch/stefan/7916125/working/building/REAL250005042893 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042893

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042893/0 /scratch/stefan/7916125/working/building/REAL250005042893 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1
`/scratch/stefan/7916125/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1)

`REAL250005042893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042893 none O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [6, 6, 6, 29, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 29, 29, 41, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17] 58
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36])
total number of confs: 189
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042893 none O=C(CCF)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [33, 33, 33, 58, 58, 17, 17, 17, 17, 17, 17, 17, 10, 17, 10, 1, 10, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 33, 17, 17, 17, 17, 17, 17, 17, 17, 10, 1] 58
rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042893 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042893
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `/scratch/stefan/7916125/finished'
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042893/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042893
Building REAL250005042894
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042894'
/scratch/stefan/7916125/working/building/REAL250005042894 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042894

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042894/0 /scratch/stefan/7916125/working/building/REAL250005042894 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/2
`/scratch/stefan/7916125/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1)

`REAL250005042894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042894 none C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 20, 20, 20, 60, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16] 99
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042894 none C[C@@H](O)C(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [33, 26, 33, 33, 26, 26, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 33, 33, 33, 99, 26, 16, 16, 16, 16, 16, 16, 16, 16, 9, 1] 99
rigid atoms, others: [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, 37])
total number of confs: 217
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042894 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042894
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042894/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042894
Building REAL250005042895
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042895'
/scratch/stefan/7916125/working/building/REAL250005042895 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042895

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042895/0 /scratch/stefan/7916125/working/building/REAL250005042895 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/3
`/scratch/stefan/7916125/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1)

`REAL250005042895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042895 none C=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18] 24
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 35, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042895 none C=CC(=O)N[C@@H]1CCCC[C@H]1NC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 18, 18, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1] 24
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 71
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042895 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042895
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042895/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042895
Building REAL250005042896
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042896'
/scratch/stefan/7916125/working/building/REAL250005042896 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042896

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042896/0 /scratch/stefan/7916125/working/building/REAL250005042896 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/4
`/scratch/stefan/7916125/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042896 none CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [135, 52, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 135, 135, 135, 135, 135, 52, 10, 10, 1, 1, 6, 27, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042896 none CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [201, 160, 160, 160, 89, 27, 27, 27, 27, 7, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 201, 160, 89, 89, 27, 27, 7, 1, 27, 27] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 788
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042896 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042896
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042896/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042896
Building REAL250005042897
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042897'
/scratch/stefan/7916125/working/building/REAL250005042897 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042897

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042897/0 /scratch/stefan/7916125/working/building/REAL250005042897 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/5
`/scratch/stefan/7916125/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042897 none COCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [167, 148, 128, 41, 41, 41, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 167, 167, 167, 148, 148, 128, 128, 41, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042897 none COCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 192, 113, 113, 113, 43, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 192, 192, 113, 43, 43, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 774
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042897 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042897
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042897/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042897
Building REAL250005042898
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042898'
/scratch/stefan/7916125/working/building/REAL250005042898 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042898

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042898/0 /scratch/stefan/7916125/working/building/REAL250005042898 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/6
`/scratch/stefan/7916125/working/3D/6' -> `0.mol2'
Preparing input files

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

`REAL250005042898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042898 none CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 1, 32, 32, 32, 32, 10, 10, 1, 1, 7, 21, 1, 1] 78
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 19, 26, 27, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 122
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042898 none CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 60, 21, 21, 21, 21, 6, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 78, 78, 78, 78, 60, 60, 21, 21, 7, 1, 21, 21] 78
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 292
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042898 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042898
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042898/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042898
Building REAL250005042899
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042899'
/scratch/stefan/7916125/working/building/REAL250005042899 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042899

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042899/0 /scratch/stefan/7916125/working/building/REAL250005042899 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/7
`/scratch/stefan/7916125/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1)

`REAL250005042899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042899 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 46, 136, 136, 46, 10, 10, 1, 1, 6, 16, 1, 1, 136, 136, 136, 136, 136] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 25, 26, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 402
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042899 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 66, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 142, 201, 201, 142, 66, 66, 16, 16, 4, 1, 16, 16, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 666
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: REAL250005042899 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 71, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 1, 1, 1, 13, 71, 71, 136, 136, 201, 201, 136, 136, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 661
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042899 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042899
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042899/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042899
Building REAL250005042900
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042900'
/scratch/stefan/7916125/working/building/REAL250005042900 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042900

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042900/0 /scratch/stefan/7916125/working/building/REAL250005042900 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/8
`/scratch/stefan/7916125/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1)

`REAL250005042900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042900 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 44, 125, 125, 125, 44, 10, 10, 1, 1, 6, 16, 1, 1, 125, 125, 125, 125, 125, 125, 125] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 374
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042900 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 57, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 120, 201, 201, 201, 120, 57, 57, 16, 16, 4, 1, 16, 16, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 651
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042900 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 55, 125, 125, 125, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 125, 1, 1, 1, 1, 11, 55, 55, 125, 125, 201, 201, 125, 125, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 652
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042900 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042900
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042900/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042900
Building REAL250005042901
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042901'
/scratch/stefan/7916125/working/building/REAL250005042901 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042901

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042901/0 /scratch/stefan/7916125/working/building/REAL250005042901 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/9
`/scratch/stefan/7916125/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042901 none O=C(CC1CC1)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 3, 1, 1, 1, 1, 23, 23, 97, 145, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 145, 3, 3, 1, 1, 1, 1, 1, 23, 97, 97, 145, 145, 201, 201, 145, 145] 201
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])
total number of confs: 690
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042901 none O=C(CC1CC1)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 115, 145, 145, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 115, 115, 145, 145, 145, 145, 145, 33, 7, 7, 1, 1, 6, 8, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 558
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042901 none O=C(CC1CC1)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 101, 165, 201, 201, 33, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 165, 165, 201, 201, 201, 201, 201, 101, 33, 33, 8, 8, 4, 1, 8, 8] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 765
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042901 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042901
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042901/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042901
Building REAL250005042902
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042902'
/scratch/stefan/7916125/working/building/REAL250005042902 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042902

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042902/0 /scratch/stefan/7916125/working/building/REAL250005042902 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/10
`/scratch/stefan/7916125/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042902 none CC(C)(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [160, 44, 160, 160, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 160, 160, 160, 160, 160, 160, 44, 8, 8, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 593
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042902 none CC(C)(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 201, 151, 151, 56, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 201, 151, 56, 56, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042902 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042902
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042902/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042902
Building REAL250005042903
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042903'
/scratch/stefan/7916125/working/building/REAL250005042903 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042903

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042903/0 /scratch/stefan/7916125/working/building/REAL250005042903 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/11
`/scratch/stefan/7916125/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042903 none COCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [144, 124, 47, 47, 47, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 144, 144, 144, 124, 124, 47, 7, 7, 1, 1, 6, 22, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 534
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042903 none COCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [201, 201, 167, 167, 167, 77, 22, 22, 22, 22, 6, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 201, 167, 77, 77, 22, 22, 6, 1, 22, 22] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 753
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042903 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042903
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042903/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042903
Building REAL250005042904
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042904'
/scratch/stefan/7916125/working/building/REAL250005042904 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042904

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042904/0 /scratch/stefan/7916125/working/building/REAL250005042904 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/12
`/scratch/stefan/7916125/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042904 none CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 131, 41, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 143, 143, 143, 143, 143, 131, 131, 41, 8, 8, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042904 none CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 123, 123, 123, 39, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 201, 201, 123, 39, 39, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042904 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042904
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042904/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042904
Building REAL250005042905
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042905'
/scratch/stefan/7916125/working/building/REAL250005042905 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042905

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042905/0 /scratch/stefan/7916125/working/building/REAL250005042905 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/13
`/scratch/stefan/7916125/working/3D/13' -> `0.mol2'
Preparing input files

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

`REAL250005042905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042905 none CC(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [136, 129, 145, 46, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 145, 145, 145, 145, 145, 145, 145, 129, 129, 46, 8, 8, 1, 1, 6, 11, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 666
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042905 none CC(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 199, 201, 143, 143, 143, 48, 11, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 201, 201, 201, 201, 199, 199, 143, 48, 48, 11, 11, 4, 1, 11, 11] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 736
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042905 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042905
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042905/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042905
Building REAL250005042906
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042906'
/scratch/stefan/7916125/working/building/REAL250005042906 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042906

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042906/0 /scratch/stefan/7916125/working/building/REAL250005042906 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/14
`/scratch/stefan/7916125/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042906 none CC1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 58, 143, 143, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 143, 2, 2, 2, 1, 1, 1, 1, 10, 58, 58, 143, 143, 201, 201, 143, 143] 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])
total number of confs: 655
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042906 none CC1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 51, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 143, 143, 143, 143, 143, 143, 143, 51, 10, 10, 1, 1, 6, 17, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 423
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: REAL250005042906 none CC1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 153, 153, 153, 59, 17, 17, 17, 17, 5, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 201, 201, 153, 59, 59, 17, 17, 5, 1, 17, 17] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 633
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042906 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042906
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042906/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042906
Building REAL250005042907
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042907'
/scratch/stefan/7916125/working/building/REAL250005042907 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042907

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042907/0 /scratch/stefan/7916125/working/building/REAL250005042907 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/15
`/scratch/stefan/7916125/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042907 none CCOCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [129, 126, 98, 43, 43, 43, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 129, 129, 129, 129, 129, 98, 98, 43, 7, 7, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 456
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042907 none CCOCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 147, 147, 147, 53, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 195, 195, 147, 53, 53, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 710
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042907 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042907
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042907/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042907
Building REAL250005042908
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042908'
/scratch/stefan/7916125/working/building/REAL250005042908 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042908

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042908/0 /scratch/stefan/7916125/working/building/REAL250005042908 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/16
`/scratch/stefan/7916125/working/3D/16' -> `0.mol2'
Preparing input files

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

`REAL250005042908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042908 none CC(C)=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 130, 53, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 130, 130, 130, 130, 130, 130, 130, 53, 10, 10, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 406
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042908 none CC(C)=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 170, 170, 170, 74, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 201, 170, 74, 74, 20, 20, 6, 1, 20, 20] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 670
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042908 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042908
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042908/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042908
Building REAL250005042909
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042909'
/scratch/stefan/7916125/working/building/REAL250005042909 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042909

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042909/0 /scratch/stefan/7916125/working/building/REAL250005042909 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/17
`/scratch/stefan/7916125/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042909 none CSCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [143, 115, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 143, 143, 143, 115, 115, 35, 7, 7, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 508
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042909 none CSCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 181, 109, 109, 109, 49, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 181, 181, 109, 49, 49, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 731
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042909 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042909
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042909/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042909
Building REAL250005042910
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042910'
/scratch/stefan/7916125/working/building/REAL250005042910 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042910

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042910/0 /scratch/stefan/7916125/working/building/REAL250005042910 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/18
`/scratch/stefan/7916125/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042910 none CCCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [145, 131, 123, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 145, 145, 145, 145, 145, 145, 145, 123, 123, 33, 7, 7, 1, 1, 6, 6, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 676
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042910 none CCCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 197, 89, 89, 89, 27, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 201, 201, 201, 201, 201, 201, 201, 197, 197, 89, 27, 27, 6, 6, 2, 1, 6, 6] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 769
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042910 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042910
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042910/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042910
Building REAL250005042911
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042911'
/scratch/stefan/7916125/working/building/REAL250005042911 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042911

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042911/0 /scratch/stefan/7916125/working/building/REAL250005042911 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/19
`/scratch/stefan/7916125/working/3D/19' -> `0.mol2'
Preparing input files

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

`REAL250005042911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042911 none CC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [156, 52, 156, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 156, 156, 156, 156, 156, 156, 156, 52, 10, 10, 1, 1, 6, 18, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 603
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042911 none CC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 161, 201, 161, 161, 69, 18, 18, 18, 18, 6, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 201, 201, 161, 69, 69, 18, 18, 6, 1, 18, 18] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 744
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042911 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042911
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042911/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042911
Building REAL250005042912
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042912'
/scratch/stefan/7916125/working/building/REAL250005042912 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042912

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042912/0 /scratch/stefan/7916125/working/building/REAL250005042912 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/20
`/scratch/stefan/7916125/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042912 none CCC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [132, 121, 46, 121, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 135, 135, 135, 135, 135, 121, 121, 121, 121, 46, 8, 8, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 569
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042912 none CCC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 124, 201, 124, 124, 42, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 42, 42, 13, 13, 3, 1, 13, 13] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 727
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042912 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042912
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042912/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042912
Building REAL250005042913
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042913'
/scratch/stefan/7916125/working/building/REAL250005042913 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042913

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042913/0 /scratch/stefan/7916125/working/building/REAL250005042913 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/21
`/scratch/stefan/7916125/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042913 none COC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 109, 50, 118, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 138, 138, 138, 118, 118, 118, 118, 50, 8, 8, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 514
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042913 none COC(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 166, 201, 166, 166, 68, 20, 20, 20, 20, 5, 20, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 201, 166, 68, 68, 20, 20, 5, 1, 20, 20] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 719
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042913 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042913
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042913/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042913
Building REAL250005042914
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042914'
/scratch/stefan/7916125/working/building/REAL250005042914 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042914

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042914/0 /scratch/stefan/7916125/working/building/REAL250005042914 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/22
`/scratch/stefan/7916125/working/3D/22' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042914 none C=CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [163, 134, 118, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 163, 163, 163, 134, 134, 118, 118, 31, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 648
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042914 none C=CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 189, 102, 102, 102, 42, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 189, 189, 102, 42, 42, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 816
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042914 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042914
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042914/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042914
Building REAL250005042915
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042915'
/scratch/stefan/7916125/working/building/REAL250005042915 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042915

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042915/0 /scratch/stefan/7916125/working/building/REAL250005042915 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/23
`/scratch/stefan/7916125/working/3D/23' -> `0.mol2'
Preparing input files

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

`REAL250005042915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042915 none CC=C(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 46, 164, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 164, 164, 164, 164, 164, 164, 164, 46, 10, 10, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 449
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042915 none CC=C(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 141, 201, 141, 141, 54, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 201, 201, 141, 54, 54, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 670
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042915 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042915
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042915/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042915
Building REAL250005042916
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042916'
/scratch/stefan/7916125/working/building/REAL250005042916 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042916

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042916/0 /scratch/stefan/7916125/working/building/REAL250005042916 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/24
`/scratch/stefan/7916125/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC[C@H]2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005042916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042916 none CC1(C(=O)NC[C@H]2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 7, 7, 43, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 137, 1, 1, 2, 2, 2, 7, 43, 43, 137, 137, 201, 201, 137, 137, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042916 none CC1(C(=O)NC[C@H]2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [137, 42, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 137, 137, 137, 137, 137, 42, 8, 8, 1, 1, 6, 12, 1, 1, 137, 137, 137, 137] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38])
total number of confs: 388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042916 none CC1(C(=O)NC[C@H]2C[C@@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 123, 123, 123, 50, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 123, 50, 50, 12, 12, 3, 1, 12, 12, 201, 201, 201, 201] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 669
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042916 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042916
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042916/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042916
Building REAL250005042917
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042917'
/scratch/stefan/7916125/working/building/REAL250005042917 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042917

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042917/0 /scratch/stefan/7916125/working/building/REAL250005042917 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/25
`/scratch/stefan/7916125/working/3D/25' -> `0.mol2'
Preparing input files

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

`REAL250005042917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042917 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 2, 2, 2, 1, 1, 11, 62, 62, 136, 136, 201, 201, 136, 136] 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])
total number of confs: 668
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042917 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [136, 136, 136, 136, 43, 136, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 136, 136, 136, 136, 136, 43, 9, 9, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042917 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 136, 201, 136, 136, 53, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 136, 53, 53, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042917 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042917
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042917/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042917
Building REAL250005042918
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042918'
/scratch/stefan/7916125/working/building/REAL250005042918 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042918

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042918/0 /scratch/stefan/7916125/working/building/REAL250005042918 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/26
`/scratch/stefan/7916125/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042918 none CCC(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 121, 46, 121, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 145, 145, 145, 145, 145, 121, 46, 8, 8, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 643
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042918 none CCC(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 140, 184, 140, 140, 43, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 184, 140, 43, 43, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042918 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042918
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042918/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042918
Building REAL250005042919
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042919'
/scratch/stefan/7916125/working/building/REAL250005042919 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042919

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042919/0 /scratch/stefan/7916125/working/building/REAL250005042919 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/27
`/scratch/stefan/7916125/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042919 none O=C(CCCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 111, 121, 164, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 111, 111, 139, 139, 157, 157, 33, 7, 7, 1, 1, 6, 6, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 784
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042919 none O=C(CCCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 190, 189, 201, 27, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 190, 190, 201, 201, 201, 201, 85, 27, 27, 6, 6, 2, 1, 6, 6] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 851
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042919 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042919
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042919/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042919
Building REAL250005042920
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042920'
/scratch/stefan/7916125/working/building/REAL250005042920 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042920

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042920/0 /scratch/stefan/7916125/working/building/REAL250005042920 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/28
`/scratch/stefan/7916125/working/3D/28' -> `0.mol2'
Preparing input files

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

`REAL250005042920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042920 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 201, 137, 2, 2, 2, 1, 1, 11, 63, 63, 137, 137, 201, 201, 137, 137] 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])
total number of confs: 671
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042920 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [137, 137, 137, 137, 44, 137, 44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 137, 137, 137, 137, 137, 44, 9, 9, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 398
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042920 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 135, 201, 135, 135, 52, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 135, 52, 52, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042920 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042920
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042920/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042920
Building REAL250005042921
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042921'
/scratch/stefan/7916125/working/building/REAL250005042921 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042921

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042921/0 /scratch/stefan/7916125/working/building/REAL250005042921 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/29
`/scratch/stefan/7916125/working/3D/29' -> `0.mol2'
Preparing input files

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

`REAL250005042921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042921 none NC(=O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [98, 50, 110, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 98, 110, 50, 8, 8, 1, 1, 6, 25, 1, 1] 180
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042921 none NC(=O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [178, 164, 180, 164, 164, 78, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 178, 180, 164, 78, 78, 25, 25, 6, 1, 25, 25] 180
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 618
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042921 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042921
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042921/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042921
Building REAL250005042922
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042922'
/scratch/stefan/7916125/working/building/REAL250005042922 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042922

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042922/0 /scratch/stefan/7916125/working/building/REAL250005042922 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/30
`/scratch/stefan/7916125/working/3D/30' -> `0.mol2'
Preparing input files

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

`REAL250005042922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042922 none CC(C)(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [77, 52, 77, 77, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 52, 10, 10, 1, 1, 7, 28, 1, 1] 136
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 320
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042922 none CC(C)(C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 129, 136, 136, 129, 129, 73, 28, 28, 28, 28, 9, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 136, 136, 136, 136, 136, 136, 136, 136, 136, 129, 73, 73, 28, 28, 9, 1, 28, 28] 136
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 478
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042922 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042922
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042922/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042922
Building REAL250005042923
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042923'
/scratch/stefan/7916125/working/building/REAL250005042923 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042923

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042923/0 /scratch/stefan/7916125/working/building/REAL250005042923 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/31
`/scratch/stefan/7916125/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042923 none C=CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [153, 101, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 153, 153, 153, 101, 101, 31, 7, 7, 1, 1, 6, 16, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 566
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042923 none C=CCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 150, 150, 150, 61, 16, 16, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 150, 61, 61, 16, 16, 6, 1, 16, 16] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042923 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042923
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042923/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042923
Building REAL250005042924
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042924'
/scratch/stefan/7916125/working/building/REAL250005042924 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005042924

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042924/0 /scratch/stefan/7916125/working/building/REAL250005042924 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/32
`/scratch/stefan/7916125/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042924 none C[NH+](C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 1, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 2, 1, 1, 2, 4, 1, 1] 9
rigid atoms, others: [35, 36, 39, 8, 9, 10, 11, 12, 13, 14, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 36
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042924 none C[NH+](C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 9, 9, 7, 4, 4, 4, 4, 4, 1, 4, 4] 9
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 33
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042924 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005042924/1 /scratch/stefan/7916125/working/building/REAL250005042924 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/33
`/scratch/stefan/7916125/working/3D/33' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042924.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005042924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042924/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042924 none CN(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [122, 115, 122, 52, 52, 52, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 122, 122, 122, 122, 122, 122, 115, 115, 52, 9, 9, 1, 1, 6, 26, 1, 1] 201
rigid atoms, others: [34, 35, 38, 7, 8, 9, 10, 11, 12, 13, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 501
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042924 none CN(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 163, 163, 163, 86, 26, 26, 26, 26, 7, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 201, 201, 201, 163, 86, 86, 26, 26, 7, 1, 26, 26] 201
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 756
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042924 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042924
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005042924/1.*
0: /scratch/stefan/7916125/working/building/REAL250005042924/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042924
Building REAL250005042925
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042925'
/scratch/stefan/7916125/working/building/REAL250005042925 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042925

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042925/0 /scratch/stefan/7916125/working/building/REAL250005042925 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/34
`/scratch/stefan/7916125/working/3D/34' -> `0.mol2'
Preparing input files

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

`REAL250005042925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042925 none C=CC(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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: [160, 100, 40, 100, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 160, 160, 160, 100, 300, 40, 7, 7, 1, 1, 6, 14, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 916
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042925 none C=CC(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 201, 157, 157, 55, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 603, 157, 55, 55, 14, 14, 4, 1, 14, 14] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1321
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042925 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042925
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042925/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042925
Building REAL250005042926
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042926'
/scratch/stefan/7916125/working/building/REAL250005042926 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042926

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042926/0 /scratch/stefan/7916125/working/building/REAL250005042926 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/35
`/scratch/stefan/7916125/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1)

`REAL250005042926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042926 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 47, 140, 140, 140, 47, 10, 10, 1, 1, 6, 12, 1, 1, 140, 140, 140, 140, 140] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042926 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [136, 136, 58, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 136, 201, 201, 201, 136, 58, 58, 12, 12, 3, 1, 12, 12, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 642
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042926 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 9, 9, 62, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 140, 1, 1, 1, 1, 9, 62, 62, 140, 140, 201, 201, 140, 140, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 656
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042926 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042926
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042926/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042926
Building REAL250005042927
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042927'
/scratch/stefan/7916125/working/building/REAL250005042927 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042927

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042927/0 /scratch/stefan/7916125/working/building/REAL250005042927 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/36
`/scratch/stefan/7916125/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042927 none CO[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [138, 109, 50, 118, 118, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 138, 138, 138, 118, 118, 118, 50, 8, 8, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 8, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 514
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042927 none CO[C@H](C)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 166, 201, 201, 166, 166, 68, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 166, 68, 68, 20, 20, 6, 1, 20, 20] 201
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 719
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042927 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042927
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042927/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042927
Building REAL250005042928
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042928'
/scratch/stefan/7916125/working/building/REAL250005042928 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042928

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042928/0 /scratch/stefan/7916125/working/building/REAL250005042928 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/37
`/scratch/stefan/7916125/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042928 none CCC=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 108, 108, 37, 37, 37, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 157, 157, 157, 157, 157, 108, 108, 37, 7, 7, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 602
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042928 none CCC=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 128, 128, 128, 48, 14, 14, 14, 14, 3, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 164, 164, 128, 48, 48, 14, 14, 3, 1, 14, 14] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 754
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042928 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042928
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042928/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042928
Building REAL250005042929
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042929'
/scratch/stefan/7916125/working/building/REAL250005042929 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005042929 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `/scratch/stefan/7916125/failed'
`/scratch/stefan/7916125/working/building/REAL250005042929' -> `/scratch/stefan/7916125/failed/REAL250005042929'
Building REAL250005042930
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042930'
/scratch/stefan/7916125/working/building/REAL250005042930 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042930

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042930/0 /scratch/stefan/7916125/working/building/REAL250005042930 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/38
`/scratch/stefan/7916125/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042930 none O=C(CO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
447  conformations in input
total number of sets (complete confs): 447
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 90, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 1, 90, 90, 270, 48, 10, 10, 1, 1, 6, 24, 1, 1] 447
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042930 none O=C(CO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
447  conformations in input
total number of sets (complete confs): 447
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 149, 79, 24, 24, 24, 24, 8, 24, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 149, 149, 447, 144, 79, 79, 24, 24, 8, 1, 24, 24] 447
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 969
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042930 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042930
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042930/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042930
Building REAL250005042931
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042931'
/scratch/stefan/7916125/working/building/REAL250005042931 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042931

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042931/0 /scratch/stefan/7916125/working/building/REAL250005042931 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/39
`/scratch/stefan/7916125/working/3D/39' -> `0.mol2'
Preparing input files

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

`REAL250005042931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042931 none CC(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [154, 50, 154, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 154, 154, 154, 154, 462, 50, 10, 10, 1, 1, 6, 22, 1, 1] 603
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 1052
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042931 none CC(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 81, 22, 22, 22, 22, 6, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 603, 173, 81, 81, 22, 22, 7, 1, 22, 22] 603
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042931 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042931
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042931/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042931
Building REAL250005042932
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042932'
/scratch/stefan/7916125/working/building/REAL250005042932 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042932

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042932/0 /scratch/stefan/7916125/working/building/REAL250005042932 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/40
`/scratch/stefan/7916125/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F)

`REAL250005042932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042932 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 44, 149, 149, 149, 44, 9, 9, 1, 1, 6, 13, 1, 1, 149, 149, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 420
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042932 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [134, 134, 52, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 134, 201, 201, 201, 134, 52, 52, 13, 13, 3, 1, 13, 13, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 631
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042932 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 72, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 149, 1, 1, 1, 1, 13, 72, 72, 149, 149, 201, 201, 149, 149, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 670
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042932 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042932
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042932/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042932
Building REAL250005042933
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042933'
/scratch/stefan/7916125/working/building/REAL250005042933 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042933

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042933/0 /scratch/stefan/7916125/working/building/REAL250005042933 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/41
`/scratch/stefan/7916125/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042933 none O=C(CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 141, 148, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 141, 141, 148, 148, 37, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 566
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042933 none O=C(CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 41, 12, 12, 12, 12, 4, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 110, 41, 41, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042933 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042933
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042933/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042933
Building REAL250005042934
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042934'
/scratch/stefan/7916125/working/building/REAL250005042934 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042934

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042934/0 /scratch/stefan/7916125/working/building/REAL250005042934 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/42
`/scratch/stefan/7916125/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042934 none O=C(C=CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 102, 102, 175, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 102, 102, 175, 175, 41, 7, 7, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042934 none O=C(C=CCF)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 199, 199, 201, 49, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 199, 199, 201, 201, 137, 49, 49, 13, 13, 3, 1, 13, 13] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 662
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042934 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042934
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042934/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042934
Building REAL250005042935
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042935'
/scratch/stefan/7916125/working/building/REAL250005042935 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042935

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042935/0 /scratch/stefan/7916125/working/building/REAL250005042935 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/43
`/scratch/stefan/7916125/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042935 none C#CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [158, 158, 132, 40, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 158, 158, 158, 132, 132, 40, 8, 8, 1, 1, 6, 9, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 632
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042935 none C#CCCC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 185, 113, 113, 113, 34, 9, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 201, 201, 201, 185, 185, 113, 34, 34, 9, 9, 3, 1, 9, 9] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 771
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042935 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042935
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042935/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042935
Building REAL250005042936
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042936'
/scratch/stefan/7916125/working/building/REAL250005042936 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042936

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042936/0 /scratch/stefan/7916125/working/building/REAL250005042936 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/44
`/scratch/stefan/7916125/working/3D/44' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1)

`REAL250005042936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042936 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 53, 130, 130, 130, 53, 10, 10, 1, 1, 6, 23, 1, 1, 130, 130, 130, 130, 130] 195
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 389
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042936 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 78, 23, 23, 23, 23, 6, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 167, 195, 195, 195, 167, 78, 78, 23, 23, 6, 1, 23, 23, 195, 195, 195, 195, 195] 195
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 640
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042936 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
195  conformations in input
total number of sets (complete confs): 195
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 58, 130, 130, 130, 130, 130, 186, 186, 186, 195, 195, 195, 195, 195, 130, 1, 1, 1, 1, 11, 58, 58, 130, 130, 186, 195, 130, 130, 1, 1, 1, 1, 1] 195
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 625
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042936 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042936
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042936/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042936
Building REAL250005042937
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042937'
/scratch/stefan/7916125/working/building/REAL250005042937 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042937

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042937/0 /scratch/stefan/7916125/working/building/REAL250005042937 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/45
`/scratch/stefan/7916125/working/3D/45' -> `0.mol2'
Preparing input files

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

`REAL250005042937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042937 none CC(C)(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [161, 49, 161, 157, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 161, 161, 161, 161, 161, 161, 483, 49, 10, 10, 1, 1, 6, 20, 1, 1] 603
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 1092
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042937 none CC(C)(O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 161, 201, 201, 161, 161, 73, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 603, 161, 73, 73, 20, 20, 6, 1, 20, 20] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1327
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042937 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042937
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042937/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042937
Building REAL250005042938
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042938'
/scratch/stefan/7916125/working/building/REAL250005042938 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042938

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042938/0 /scratch/stefan/7916125/working/building/REAL250005042938 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/46
`/scratch/stefan/7916125/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042938 none CC1=CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 76, 152, 152, 152, 152, 152, 201, 201, 201, 201, 201, 201, 201, 201, 152, 2, 2, 2, 1, 1, 13, 76, 76, 152, 152, 201, 201, 152, 152] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 684
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042938 none CC1=CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [152, 152, 152, 42, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 152, 152, 152, 152, 152, 42, 8, 8, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042938 none CC1=CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 120, 120, 120, 48, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 120, 48, 48, 13, 13, 3, 1, 13, 13] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 626
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042938 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042938
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042938/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042938
Building REAL250005042939
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042939'
/scratch/stefan/7916125/working/building/REAL250005042939 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042939

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042939/0 /scratch/stefan/7916125/working/building/REAL250005042939 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/47
`/scratch/stefan/7916125/working/3D/47' -> `0.mol2'
Preparing input files

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

`REAL250005042939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042939 none C[C@@H](O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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: [153, 51, 153, 152, 51, 51, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 153, 153, 153, 459, 51, 10, 10, 1, 1, 6, 23, 1, 1] 603
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 1047
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042939 none C[C@@H](O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 174, 201, 201, 174, 174, 84, 23, 23, 23, 23, 6, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 603, 174, 84, 84, 23, 23, 7, 1, 23, 23] 603
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1311
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042939 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042939
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042939/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042939
Building REAL250005042940
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042940'
/scratch/stefan/7916125/working/building/REAL250005042940 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042940

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042940/0 /scratch/stefan/7916125/working/building/REAL250005042940 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/48
`/scratch/stefan/7916125/working/3D/48' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042940 none O=C(C=CCO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 105, 105, 167, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 105, 105, 167, 167, 501, 41, 7, 7, 1, 1, 6, 12, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 1127
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042940 none O=C(C=CCO)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
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: [137, 137, 137, 195, 195, 201, 51, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 195, 195, 201, 201, 603, 137, 51, 51, 12, 12, 3, 1, 12, 12] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1252
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042940 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042940
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042940/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042940
Building REAL250005042941
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042941'
/scratch/stefan/7916125/working/building/REAL250005042941 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042941

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042941/0 /scratch/stefan/7916125/working/building/REAL250005042941 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/49
`/scratch/stefan/7916125/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005042941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042941 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 46, 84, 84, 84, 46, 8, 8, 1, 1, 6, 26, 1, 1, 84, 84, 84, 84, 84] 128
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 224
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042941 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 60, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 128, 128, 128, 128, 128, 60, 60, 26, 26, 8, 1, 26, 26, 128, 128, 128, 128, 128] 128
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 426
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042941 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 40, 84, 84, 84, 84, 84, 120, 120, 120, 128, 128, 128, 128, 128, 84, 1, 1, 1, 1, 11, 40, 40, 84, 84, 120, 128, 84, 84, 1, 1, 1, 1, 1] 128
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 413
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042941 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042941
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042941/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042941
Building REAL250005042942
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042942'
/scratch/stefan/7916125/working/building/REAL250005042942 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042942

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042942/0 /scratch/stefan/7916125/working/building/REAL250005042942 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/50
`/scratch/stefan/7916125/working/3D/50' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042942 none CON=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [135, 107, 107, 48, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 135, 135, 135, 107, 48, 8, 8, 1, 1, 6, 26, 1, 1] 188
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 393
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042942 none CON=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 188, 168, 168, 168, 90, 26, 26, 26, 26, 6, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 188, 188, 188, 188, 168, 90, 90, 26, 26, 6, 1, 26, 26] 188
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 650
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042942 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042942
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042942/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042942
Building REAL250005042943
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042943'
/scratch/stefan/7916125/working/building/REAL250005042943 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042943

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042943/0 /scratch/stefan/7916125/working/building/REAL250005042943 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/51
`/scratch/stefan/7916125/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1)

`REAL250005042943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042943 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 45, 156, 156, 156, 45, 9, 9, 1, 1, 6, 14, 1, 1, 156, 156, 156, 156] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 439
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042943 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 53, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 153, 201, 201, 201, 153, 53, 53, 14, 14, 4, 1, 14, 14, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 633
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042943 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 71, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 1, 1, 1, 1, 11, 71, 71, 156, 156, 201, 201, 156, 156, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 657
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042943 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042943
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042943/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042943
Building REAL250005042944
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042944'
/scratch/stefan/7916125/working/building/REAL250005042944 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042944

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042944/0 /scratch/stefan/7916125/working/building/REAL250005042944 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/52
`/scratch/stefan/7916125/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042944 none CC=C(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [154, 154, 48, 152, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 154, 154, 154, 154, 48, 8, 8, 1, 1, 6, 22, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 445
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042944 none CC=C(F)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 173, 201, 173, 173, 70, 22, 22, 22, 22, 6, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 173, 70, 70, 22, 22, 6, 1, 22, 22] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 644
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042944 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042944
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042944/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042944
Building REAL250005042945
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042945'
/scratch/stefan/7916125/working/building/REAL250005042945 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042945

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042945/0 /scratch/stefan/7916125/working/building/REAL250005042945 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/53
`/scratch/stefan/7916125/working/3D/53' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042945 none CC(CO)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [126, 43, 126, 157, 43, 43, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 126, 126, 126, 126, 157, 157, 471, 43, 7, 7, 1, 1, 6, 14, 1, 1] 603
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 1126
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042945 none CC(CO)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 132, 201, 201, 132, 132, 50, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 201, 603, 132, 50, 50, 14, 14, 4, 1, 14, 14] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1345
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042945 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042945
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042945/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042945
Building REAL250005042946
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042946'
/scratch/stefan/7916125/working/building/REAL250005042946 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042946

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042946/0 /scratch/stefan/7916125/working/building/REAL250005042946 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/54
`/scratch/stefan/7916125/working/3D/54' -> `0.mol2'
Preparing input files

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

`REAL250005042946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042946 none C[C@H](O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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: [153, 50, 153, 153, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 153, 153, 153, 459, 50, 10, 10, 1, 1, 6, 23, 1, 1] 603
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 1050
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042946 none C[C@H](O)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 174, 201, 201, 174, 174, 84, 23, 23, 23, 23, 7, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 603, 174, 84, 84, 23, 23, 7, 1, 23, 23] 603
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1306
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042946 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042946
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042946/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042946
Building REAL250005042947
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042947'
/scratch/stefan/7916125/working/building/REAL250005042947 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042947

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042947/0 /scratch/stefan/7916125/working/building/REAL250005042947 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/55
`/scratch/stefan/7916125/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042947 none C=C1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 12, 12, 12, 74, 162, 162, 162, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 162, 1, 1, 1, 1, 1, 12, 74, 74, 162, 162, 201, 201, 162, 162] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 662
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042947 none C=C1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [162, 162, 162, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 162, 162, 162, 162, 162, 43, 9, 9, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 442
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042947 none C=C1CC1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 122, 122, 122, 49, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 122, 49, 49, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042947 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042947
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042947/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042947
Building REAL250005042948
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042948'
/scratch/stefan/7916125/working/building/REAL250005042948 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042948

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042948/0 /scratch/stefan/7916125/working/building/REAL250005042948 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/56
`/scratch/stefan/7916125/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042948 none CC(CF)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 114, 159, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 114, 114, 114, 114, 159, 159, 40, 7, 7, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 700
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042948 none CC(CF)C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 138, 199, 201, 138, 138, 49, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 199, 199, 199, 199, 201, 201, 138, 49, 49, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042948 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042948
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042948/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042948
Building REAL250005042949
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042949'
/scratch/stefan/7916125/working/building/REAL250005042949 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042949

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042949/0 /scratch/stefan/7916125/working/building/REAL250005042949 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/57
`/scratch/stefan/7916125/working/3D/57' -> `0.mol2'
Preparing input files

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

`REAL250005042949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042949 none C=C(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [145, 115, 145, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 145, 145, 145, 145, 145, 115, 115, 31, 7, 7, 1, 1, 6, 16, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 541
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042949 none C=C(C)CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 201, 124, 124, 124, 54, 16, 16, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 199, 199, 124, 54, 54, 16, 16, 6, 1, 16, 16] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042949 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042949
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042949/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042949
Building REAL250005042950
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042950'
/scratch/stefan/7916125/working/building/REAL250005042950 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042950

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042950/0 /scratch/stefan/7916125/working/building/REAL250005042950 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/58
`/scratch/stefan/7916125/working/3D/58' -> `0.mol2'
Preparing input files

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

`REAL250005042950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042950 none CC=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [141, 141, 56, 56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 141, 141, 141, 141, 141, 56, 10, 10, 1, 1, 6, 26, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 430
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042950 none CC=CC(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 171, 171, 171, 96, 26, 26, 26, 26, 6, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 171, 96, 96, 26, 26, 7, 1, 26, 26] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 690
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042950 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042950
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042950/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042950
Building REAL250005042951
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042951'
/scratch/stefan/7916125/working/building/REAL250005042951 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042951

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042951/0 /scratch/stefan/7916125/working/building/REAL250005042951 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/59
`/scratch/stefan/7916125/working/3D/59' -> `0.mol2'
Preparing input files

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

`REAL250005042951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042951 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 2, 2, 2, 1, 1, 11, 62, 62, 136, 136, 201, 201, 136, 136] 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])
total number of confs: 668
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042951 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [136, 136, 136, 136, 43, 136, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 136, 136, 136, 136, 136, 43, 9, 9, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 396
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042951 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 136, 201, 136, 136, 53, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 136, 53, 53, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 644
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042951 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042951
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042951/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042951
Building REAL250005042952
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042952'
/scratch/stefan/7916125/working/building/REAL250005042952 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042952

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042952/0 /scratch/stefan/7916125/working/building/REAL250005042952 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/60
`/scratch/stefan/7916125/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1)

`REAL250005042952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042952 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [49, 49, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 49, 155, 155, 155, 49, 9, 9, 1, 1, 6, 16, 1, 1, 465, 155, 155, 155, 155] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 912
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042952 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 58, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 164, 201, 201, 201, 164, 58, 58, 16, 16, 4, 1, 16, 16, 603, 201, 201, 201, 201] 603
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1222
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042952 none O=C(NC[C@H]1C[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 69, 155, 155, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 201, 155, 1, 1, 1, 1, 11, 69, 69, 155, 155, 201, 201, 155, 155, 6, 1, 1, 1, 1] 603
rigid atoms, others: [1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 665
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042952 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042952
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042952/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042952
Building REAL250005042953
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042953'
/scratch/stefan/7916125/working/building/REAL250005042953 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042953

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042953/0 /scratch/stefan/7916125/working/building/REAL250005042953 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/61
`/scratch/stefan/7916125/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042953 none O=C(CC1CC1)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 3, 1, 1, 1, 1, 22, 22, 73, 73, 73, 73, 73, 156, 201, 201, 201, 201, 201, 201, 201, 201, 73, 3, 3, 1, 1, 1, 1, 1, 22, 73, 73, 156, 156, 201, 201, 73, 73] 201
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])
total number of confs: 732
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042953 none O=C(CC1CC1)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 46, 73, 73, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 41, 41, 41, 41, 41, 1, 46, 46, 73, 73, 73, 73, 73, 6, 1, 1, 9, 9, 39, 41, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 359
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042953 none O=C(CC1CC1)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 100, 100, 174, 201, 201, 41, 41, 41, 41, 11, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 174, 174, 201, 201, 201, 201, 201, 100, 41, 41, 10, 10, 3, 1, 41, 41] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 787
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042953 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042953
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042953/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042953
Building REAL250005042954
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042954'
/scratch/stefan/7916125/working/building/REAL250005042954 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042954

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042954/0 /scratch/stefan/7916125/working/building/REAL250005042954 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/62
`/scratch/stefan/7916125/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042954 none CC(C)(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 40, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 52, 75, 75, 75, 75, 75, 1, 40, 40, 40, 40, 40, 40, 6, 1, 1, 9, 9, 52, 75, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 303
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042954 none CC(C)(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 155, 155, 75, 75, 75, 75, 21, 75, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 201, 155, 75, 75, 21, 21, 4, 1, 75, 75] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 721
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042954 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042954
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042954/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042954
Building REAL250005042955
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042955'
/scratch/stefan/7916125/working/building/REAL250005042955 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042955

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042955/0 /scratch/stefan/7916125/working/building/REAL250005042955 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/63
`/scratch/stefan/7916125/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042955 none COCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [70, 46, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 52, 52, 52, 52, 52, 1, 70, 70, 70, 46, 46, 6, 1, 1, 9, 9, 48, 52, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 320
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042955 none COCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [201, 201, 138, 138, 138, 52, 52, 52, 52, 14, 52, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 138, 52, 52, 13, 13, 4, 1, 52, 52] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 719
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042955 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042955
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042955/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042955
Building REAL250005042956
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042956'
/scratch/stefan/7916125/working/building/REAL250005042956 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042956

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042956/0 /scratch/stefan/7916125/working/building/REAL250005042956 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/64
`/scratch/stefan/7916125/working/3D/64' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042956 none CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 44, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 47, 47, 47, 47, 47, 1, 63, 63, 63, 63, 63, 44, 44, 6, 1, 1, 9, 9, 43, 47, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 37, 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, 32, 33, 34, 35])
total number of confs: 448
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042956 none CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 114, 114, 114, 47, 47, 47, 47, 13, 47, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 197, 197, 114, 47, 47, 12, 12, 4, 1, 47, 47] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 777
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042956 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042956
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042956/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042956
Building REAL250005042957
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042957'
/scratch/stefan/7916125/working/building/REAL250005042957 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042957

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042957/0 /scratch/stefan/7916125/working/building/REAL250005042957 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/65
`/scratch/stefan/7916125/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042957 none CC(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 27, 36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 59, 59, 59, 59, 59, 1, 36, 36, 36, 36, 36, 36, 36, 27, 27, 6, 1, 1, 9, 9, 48, 59, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 325
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042957 none CC(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [200, 201, 201, 120, 120, 120, 59, 59, 59, 59, 19, 59, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 59, 59, 19, 19, 4, 1, 59, 59] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 746
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042957 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042957
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042957/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042957
Building REAL250005042958
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042958'
/scratch/stefan/7916125/working/building/REAL250005042958 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042958

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042958/0 /scratch/stefan/7916125/working/building/REAL250005042958 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/66
`/scratch/stefan/7916125/working/3D/66' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042958 none CC1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 33, 33, 33, 33, 33, 136, 201, 201, 201, 201, 201, 201, 201, 201, 33, 2, 2, 2, 1, 1, 1, 1, 9, 33, 33, 136, 136, 201, 201, 33, 33] 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])
total number of confs: 715
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042958 none CC1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 55, 77, 77, 77, 77, 77, 1, 33, 33, 33, 33, 33, 33, 33, 6, 1, 1, 10, 10, 55, 77, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042958 none CC1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 150, 150, 150, 77, 77, 77, 77, 23, 77, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 150, 77, 77, 23, 23, 4, 1, 77, 77] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 631
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042958 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042958
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042958/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042958
Building REAL250005042959
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042959'
/scratch/stefan/7916125/working/building/REAL250005042959 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042959

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042959/0 /scratch/stefan/7916125/working/building/REAL250005042959 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/67
`/scratch/stefan/7916125/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042959 none CCOCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [64, 62, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 51, 51, 51, 51, 51, 1, 64, 64, 64, 64, 64, 30, 30, 6, 1, 1, 9, 9, 46, 51, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042959 none CCOCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 130, 130, 130, 51, 51, 51, 51, 15, 51, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 200, 200, 130, 51, 51, 14, 14, 3, 1, 51, 51] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 734
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042959 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042959
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042959/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042959
Building REAL250005042960
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042960'
/scratch/stefan/7916125/working/building/REAL250005042960 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042960

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042960/0 /scratch/stefan/7916125/working/building/REAL250005042960 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/68
`/scratch/stefan/7916125/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042960 none CC(C)=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 57, 90, 90, 90, 90, 90, 1, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 10, 10, 57, 90, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 270
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042960 none CC(C)=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 167, 167, 167, 90, 90, 90, 90, 29, 90, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 167, 90, 90, 29, 29, 6, 1, 90, 90] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 633
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042960 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042960
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042960/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042960
Building REAL250005042961
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042961'
/scratch/stefan/7916125/working/building/REAL250005042961 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042961

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042961/0 /scratch/stefan/7916125/working/building/REAL250005042961 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/69
`/scratch/stefan/7916125/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042961 none CSCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [89, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 38, 38, 38, 40, 40, 40, 40, 40, 1, 86, 89, 89, 40, 40, 6, 1, 1, 9, 9, 38, 40, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 311
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042961 none CSCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 188, 109, 109, 109, 40, 40, 40, 40, 10, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 188, 188, 109, 40, 40, 10, 10, 3, 1, 40, 40] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042961 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042961
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042961/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042961
Building REAL250005042962
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042962'
/scratch/stefan/7916125/working/building/REAL250005042962 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042962

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042962/0 /scratch/stefan/7916125/working/building/REAL250005042962 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/70
`/scratch/stefan/7916125/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042962 none CCCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 59, 44, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 35, 35, 35, 35, 1, 70, 70, 70, 70, 70, 70, 70, 44, 44, 6, 1, 1, 9, 9, 35, 35, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042962 none CCCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 91, 91, 91, 35, 35, 35, 35, 8, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 201, 201, 201, 191, 191, 91, 35, 35, 8, 8, 2, 1, 35, 35] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 760
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042962 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042962
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042962/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042962
Building REAL250005042963
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042963'
/scratch/stefan/7916125/working/building/REAL250005042963 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042963

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042963/0 /scratch/stefan/7916125/working/building/REAL250005042963 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/71
`/scratch/stefan/7916125/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042963 none CC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 60, 60, 60, 94, 94, 94, 94, 94, 1, 35, 35, 35, 35, 35, 35, 35, 6, 1, 1, 10, 10, 60, 94, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 37, 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, 32, 33, 34, 35])
total number of confs: 328
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042963 none CC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 168, 201, 168, 168, 94, 94, 94, 94, 24, 94, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 168, 94, 94, 24, 24, 3, 1, 94, 94] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 700
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042963 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042963
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042963/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042963
Building REAL250005042964
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042964'
/scratch/stefan/7916125/working/building/REAL250005042964 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042964

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042964/0 /scratch/stefan/7916125/working/building/REAL250005042964 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/72
`/scratch/stefan/7916125/working/3D/72' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042964 none CCC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 51, 51, 51, 51, 51, 1, 43, 43, 43, 43, 43, 32, 32, 32, 32, 6, 1, 1, 9, 9, 43, 51, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 310
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042964 none CCC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 126, 198, 126, 126, 51, 51, 51, 51, 17, 51, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 198, 198, 198, 198, 126, 51, 51, 16, 16, 4, 1, 51, 51] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 728
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042964 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042964
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042964/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042964
Building REAL250005042965
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042965'
/scratch/stefan/7916125/working/building/REAL250005042965 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042965

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042965/0 /scratch/stefan/7916125/working/building/REAL250005042965 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/73
`/scratch/stefan/7916125/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042965 none COC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 59, 59, 59, 59, 59, 1, 58, 58, 58, 43, 43, 43, 43, 6, 1, 1, 9, 9, 51, 59, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 310
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042965 none COC(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 151, 151, 59, 59, 59, 59, 14, 59, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 151, 59, 59, 13, 13, 3, 1, 59, 59] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 683
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042965 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042965
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042965/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042965
Building REAL250005042966
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042966'
/scratch/stefan/7916125/working/building/REAL250005042966 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042966

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042966/0 /scratch/stefan/7916125/working/building/REAL250005042966 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/74
`/scratch/stefan/7916125/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042966 none C=CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 41, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 33, 33, 33, 60, 60, 60, 60, 60, 1, 82, 82, 82, 41, 41, 40, 40, 6, 1, 1, 5, 5, 33, 60, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 405
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042966 none C=CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 133, 133, 133, 60, 60, 60, 60, 23, 60, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 200, 200, 133, 60, 60, 23, 23, 3, 1, 60, 60] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 752
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042966 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042966
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042966/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042966
Building REAL250005042967
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042967'
/scratch/stefan/7916125/working/building/REAL250005042967 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042967

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042967/0 /scratch/stefan/7916125/working/building/REAL250005042967 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/75
`/scratch/stefan/7916125/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042967 none CC(C#N)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 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: [47, 6, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 57, 57, 57, 57, 57, 1, 47, 47, 47, 47, 6, 1, 1, 9, 9, 51, 57, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 290
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042967 none CC(C#N)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 139, 201, 201, 139, 139, 57, 57, 57, 57, 15, 57, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 139, 57, 57, 15, 15, 3, 1, 57, 57] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 703
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042967 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042967
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042967/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042967
Building REAL250005042968
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042968'
/scratch/stefan/7916125/working/building/REAL250005042968 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042968

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042968/0 /scratch/stefan/7916125/working/building/REAL250005042968 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/76
`/scratch/stefan/7916125/working/3D/76' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042968 none CC=C(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 6, 42, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 52, 65, 65, 65, 65, 65, 1, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 9, 9, 52, 65, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 250
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042968 none CC=C(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 201, 149, 149, 65, 65, 65, 65, 20, 65, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 149, 65, 65, 20, 20, 4, 1, 65, 65] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 632
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042968 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042968
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042968/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042968
Building REAL250005042969
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042969'
/scratch/stefan/7916125/working/building/REAL250005042969 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042969

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042969/0 /scratch/stefan/7916125/working/building/REAL250005042969 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/77
`/scratch/stefan/7916125/working/3D/77' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042969 none CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [48, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 59, 59, 59, 102, 102, 102, 102, 102, 1, 48, 48, 48, 48, 48, 6, 1, 1, 10, 10, 59, 102, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 20, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 375
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042969 none CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [201, 171, 171, 171, 102, 102, 102, 102, 34, 102, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 171, 102, 102, 34, 34, 7, 1, 102, 102] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 713
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042969 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042969
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042969/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042969
Building REAL250005042970
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042970'
/scratch/stefan/7916125/working/building/REAL250005042970 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042970

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042970/0 /scratch/stefan/7916125/working/building/REAL250005042970 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/78
`/scratch/stefan/7916125/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042970 none COCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 56, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 32, 32, 32, 42, 42, 42, 42, 42, 1, 69, 69, 69, 56, 56, 40, 40, 6, 1, 1, 6, 6, 32, 42, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 350
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042970 none COCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 194, 107, 107, 107, 42, 42, 42, 42, 19, 42, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 201, 194, 194, 107, 42, 42, 19, 19, 4, 1, 42, 42] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042970 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042970
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042970/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042970
Building REAL250005042971
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042971'
/scratch/stefan/7916125/working/building/REAL250005042971 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042971

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042971/0 /scratch/stefan/7916125/working/building/REAL250005042971 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/79
`/scratch/stefan/7916125/working/3D/79' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042971 none CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 49, 79, 79, 79, 79, 79, 1, 6, 6, 6, 6, 1, 1, 10, 10, 49, 79, 1, 1] 87
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 19, 24, 25, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29])
total number of confs: 186
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042971 none CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 79, 79, 79, 79, 40, 79, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 87, 87, 87, 87, 79, 79, 40, 40, 9, 1, 79, 79] 87
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 282
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042971 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042971
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042971/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042971
Building REAL250005042972
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042972'
/scratch/stefan/7916125/working/building/REAL250005042972 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042972

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042972/0 /scratch/stefan/7916125/working/building/REAL250005042972 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/80
`/scratch/stefan/7916125/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005042972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042972 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [55, 55, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 1, 55, 75, 75, 75, 75, 75, 55, 9, 9, 1, 1, 6, 44, 44, 44, 44, 44, 1, 1, 75] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 15, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 270
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042972 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 43, 43, 43, 12, 43, 12, 1, 12, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 130, 130, 43, 43, 12, 1, 1, 1, 1, 1, 43, 43, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 706
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: REAL250005042972 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 24, 74, 74, 74, 74, 74, 141, 141, 141, 201, 201, 74, 1, 1, 1, 1, 1, 1, 4, 24, 24, 74, 74, 141, 201, 201, 201, 201, 201, 74, 74, 1] 201
rigid atoms, others: [1, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 620
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042972 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042972
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042972/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042972
Building REAL250005042973
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042973'
/scratch/stefan/7916125/working/building/REAL250005042973 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042973

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042973/0 /scratch/stefan/7916125/working/building/REAL250005042973 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/81
`/scratch/stefan/7916125/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1)

`REAL250005042973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042973 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 40, 40, 40, 1, 48, 71, 71, 71, 71, 71, 48, 10, 10, 1, 1, 6, 40, 40, 40, 40, 40, 40, 40, 1, 1, 71] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 16, 36, 26, 27, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 253
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042973 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 40, 40, 40, 40, 11, 40, 11, 1, 11, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 119, 119, 40, 40, 11, 1, 1, 1, 1, 1, 1, 1, 40, 40, 201] 201
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38])
total number of confs: 690
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: REAL250005042973 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 22, 71, 71, 71, 71, 71, 123, 123, 123, 201, 201, 201, 71, 1, 1, 1, 1, 1, 1, 4, 22, 22, 71, 71, 123, 201, 201, 201, 201, 201, 201, 201, 71, 71, 1] 201
rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 618
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042973 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042973
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042973/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042973
Building REAL250005042974
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042974'
/scratch/stefan/7916125/working/building/REAL250005042974 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042974

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042974/0 /scratch/stefan/7916125/working/building/REAL250005042974 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/82
`/scratch/stefan/7916125/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042974 none NC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 55, 69, 69, 69, 69, 69, 1, 29, 34, 6, 1, 1, 10, 10, 55, 69, 1, 1] 157
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 21, 25, 26, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 249
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042974 none NC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
157  conformations in input
total number of sets (complete confs): 157
using faster count positions algorithm for large data
unique positions, atoms: [157, 146, 157, 146, 146, 69, 69, 69, 69, 21, 69, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 69, 157, 157, 146, 69, 69, 20, 20, 3, 1, 69, 69] 157
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 464
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042974 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042974
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042974/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042974
Building REAL250005042975
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042975'
/scratch/stefan/7916125/working/building/REAL250005042975 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042975

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042975/0 /scratch/stefan/7916125/working/building/REAL250005042975 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/83
`/scratch/stefan/7916125/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042975 none CC(C)(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 61, 61, 61, 120, 120, 120, 120, 120, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 1, 10, 10, 61, 120, 1, 1] 163
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 303
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042975 none CC(C)(C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
163  conformations in input
total number of sets (complete confs): 163
using faster count positions algorithm for large data
unique positions, atoms: [163, 153, 163, 163, 153, 153, 120, 120, 120, 120, 45, 120, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 120, 163, 163, 163, 163, 163, 163, 163, 163, 163, 153, 120, 120, 44, 44, 8, 1, 120, 120] 163
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 537
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042975 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042975
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042975/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042975
Building REAL250005042976
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042976'
/scratch/stefan/7916125/working/building/REAL250005042976 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042976

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042976/0 /scratch/stefan/7916125/working/building/REAL250005042976 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/84
`/scratch/stefan/7916125/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N[C@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005042976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042976 none CC1(C(=O)N[C@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 130, 201, 201, 201, 201, 201, 201, 201, 201, 28, 1, 1, 2, 2, 2, 7, 28, 28, 130, 130, 201, 201, 28, 28, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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])
total number of confs: 712
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042976 none CC1(C(=O)N[C@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 72, 72, 72, 72, 72, 1, 28, 28, 28, 28, 28, 6, 1, 1, 9, 9, 51, 72, 1, 1, 28, 28, 28, 28] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 20, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 235
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: REAL250005042976 none CC1(C(=O)N[C@H]2C[C@@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 134, 134, 134, 72, 72, 72, 72, 21, 72, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 134, 72, 72, 21, 21, 3, 1, 72, 72, 201, 201, 201, 201] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 656
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042976 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042976
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042976/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042976
Building REAL250005042977
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042977'
/scratch/stefan/7916125/working/building/REAL250005042977 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042977

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042977/0 /scratch/stefan/7916125/working/building/REAL250005042977 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/85
`/scratch/stefan/7916125/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042977 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 44, 44, 44, 44, 144, 201, 201, 201, 201, 201, 201, 201, 201, 44, 2, 2, 2, 1, 1, 12, 44, 44, 144, 144, 201, 201, 44, 44] 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])
total number of confs: 719
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042977 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [44, 44, 44, 44, 6, 44, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 65, 65, 65, 65, 65, 1, 44, 44, 44, 44, 44, 6, 1, 1, 9, 9, 48, 65, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
total number of confs: 253
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: REAL250005042977 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 128, 201, 128, 128, 65, 65, 65, 65, 20, 65, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 128, 65, 65, 20, 20, 4, 1, 65, 65] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 622
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042977 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042977
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042977/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042977
Building REAL250005042978
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042978'
/scratch/stefan/7916125/working/building/REAL250005042978 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042978

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042978/0 /scratch/stefan/7916125/working/building/REAL250005042978 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/86
`/scratch/stefan/7916125/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042978 none CCC(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 45, 45, 45, 55, 55, 55, 55, 55, 1, 62, 62, 62, 62, 62, 38, 6, 1, 1, 9, 9, 45, 55, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 435
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042978 none CCC(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 133, 182, 133, 133, 55, 55, 55, 55, 18, 55, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 182, 133, 55, 55, 17, 17, 4, 1, 55, 55] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 751
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042978 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042978
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042978/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042978
Building REAL250005042979
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042979'
/scratch/stefan/7916125/working/building/REAL250005042979 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042979

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042979/0 /scratch/stefan/7916125/working/building/REAL250005042979 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/87
`/scratch/stefan/7916125/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042979 none O=C(CCCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 41, 54, 85, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25, 25, 25, 1, 41, 41, 70, 70, 77, 81, 6, 1, 1, 7, 7, 25, 25, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 501
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042979 none O=C(CCCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 171, 196, 201, 25, 25, 25, 25, 8, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 171, 171, 201, 201, 201, 201, 81, 25, 25, 8, 8, 2, 1, 25, 25] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 834
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042979 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042979
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042979/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042979
Building REAL250005042980
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042980'
/scratch/stefan/7916125/working/building/REAL250005042980 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042980

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042980/0 /scratch/stefan/7916125/working/building/REAL250005042980 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/88
`/scratch/stefan/7916125/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)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042980 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 39, 39, 135, 201, 201, 201, 201, 201, 201, 201, 201, 39, 2, 2, 2, 1, 1, 11, 39, 39, 135, 135, 201, 201, 39, 39] 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])
total number of confs: 720
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042980 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [39, 39, 39, 39, 6, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 62, 62, 62, 62, 62, 1, 39, 39, 39, 39, 39, 6, 1, 1, 9, 9, 44, 62, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
total number of confs: 237
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: REAL250005042980 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 134, 201, 134, 134, 62, 62, 62, 62, 19, 62, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 134, 62, 62, 19, 19, 3, 1, 62, 62] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 620
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042980 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042980
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042980/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042980
Building REAL250005042981
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042981'
/scratch/stefan/7916125/working/building/REAL250005042981 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042981

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042981/0 /scratch/stefan/7916125/working/building/REAL250005042981 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/89
`/scratch/stefan/7916125/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042981 none O=C(CO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
501  conformations in input
total number of sets (complete confs): 501
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 52, 1, 1, 1, 1, 1, 1, 1, 10, 60, 60, 60, 98, 98, 98, 98, 98, 1, 52, 52, 156, 6, 1, 1, 10, 10, 60, 98, 1, 1] 501
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 534
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042981 none O=C(CO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
501  conformations in input
total number of sets (complete confs): 501
using faster count positions algorithm for large data
unique positions, atoms: [157, 157, 157, 167, 98, 98, 98, 98, 32, 98, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 98, 167, 167, 501, 157, 98, 98, 31, 31, 6, 1, 98, 98] 501
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 1042
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042981 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042981
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042981/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042981
Building REAL250005042982
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042982'
/scratch/stefan/7916125/working/building/REAL250005042982 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042982

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042982/0 /scratch/stefan/7916125/working/building/REAL250005042982 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/90
`/scratch/stefan/7916125/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1)

`REAL250005042982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042982 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 42, 42, 42, 1, 56, 91, 91, 91, 91, 91, 56, 10, 10, 1, 1, 6, 42, 42, 42, 42, 42, 1, 1, 91] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 296
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042982 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 127, 42, 42, 42, 42, 12, 42, 12, 1, 12, 1, 1, 1, 1, 42, 198, 201, 201, 201, 201, 201, 198, 127, 127, 42, 42, 12, 1, 1, 1, 1, 1, 42, 42, 201] 201
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 700
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: REAL250005042982 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 34, 91, 91, 91, 91, 91, 167, 167, 167, 201, 201, 201, 91, 1, 1, 1, 1, 1, 1, 7, 34, 34, 91, 91, 167, 201, 201, 201, 201, 201, 91, 91, 1] 201
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 636
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042982 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042982
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042982/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042982
Building REAL250005042983
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042983'
/scratch/stefan/7916125/working/building/REAL250005042983 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042983

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042983/0 /scratch/stefan/7916125/working/building/REAL250005042983 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/91
`/scratch/stefan/7916125/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1)

`REAL250005042983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042983 none O=C(NC[C@@H]1C[C@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 37, 37, 1, 48, 70, 70, 70, 70, 70, 48, 10, 10, 1, 1, 6, 37, 37, 37, 37, 37, 1, 1, 70] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 251
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042983 none O=C(NC[C@@H]1C[C@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 37, 37, 37, 37, 11, 37, 11, 1, 11, 1, 1, 1, 1, 37, 201, 201, 201, 201, 201, 201, 201, 129, 129, 37, 37, 11, 1, 1, 1, 1, 1, 37, 37, 201] 201
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 713
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: REAL250005042983 none O=C(NC[C@@H]1C[C@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 70, 70, 70, 70, 70, 141, 141, 141, 201, 201, 201, 70, 1, 1, 1, 1, 1, 1, 3, 21, 21, 70, 70, 141, 201, 201, 201, 201, 201, 70, 70, 1] 201
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 637
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042983 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042983
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042983/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042983
Building REAL250005042984
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042984'
/scratch/stefan/7916125/working/building/REAL250005042984 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042984

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042984/0 /scratch/stefan/7916125/working/building/REAL250005042984 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/92
`/scratch/stefan/7916125/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042984 none O=C(C=CCO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 24, 24, 74, 1, 1, 1, 1, 1, 1, 1, 8, 43, 43, 43, 68, 68, 68, 68, 68, 1, 24, 24, 74, 74, 222, 6, 1, 1, 8, 8, 43, 68, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 642
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042984 none O=C(C=CCO)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
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: [148, 148, 148, 200, 200, 201, 68, 68, 68, 68, 24, 68, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 68, 200, 200, 201, 201, 603, 148, 68, 68, 23, 23, 4, 1, 68, 68] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1240
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042984 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042984
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042984/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042984
Building REAL250005042985
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042985'
/scratch/stefan/7916125/working/building/REAL250005042985 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042985

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042985/0 /scratch/stefan/7916125/working/building/REAL250005042985 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/93
`/scratch/stefan/7916125/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042985 none CCC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 51, 51, 51, 51, 51, 1, 59, 59, 59, 59, 59, 29, 29, 6, 1, 1, 9, 9, 47, 51, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 356
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042985 none CCC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 143, 143, 115, 115, 115, 51, 51, 51, 51, 14, 51, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 143, 143, 115, 51, 51, 13, 13, 4, 1, 51, 51] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 788
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042985 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042985
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042985/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042985
Building REAL250005042986
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042986'
/scratch/stefan/7916125/working/building/REAL250005042986 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042986

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042986/0 /scratch/stefan/7916125/working/building/REAL250005042986 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/94
`/scratch/stefan/7916125/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042986 none C#CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [71, 71, 44, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 44, 44, 44, 44, 44, 1, 71, 71, 71, 44, 44, 6, 1, 1, 9, 9, 42, 44, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 413
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042986 none C#CCCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 189, 107, 107, 107, 44, 44, 44, 44, 12, 44, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 189, 189, 107, 44, 44, 11, 11, 3, 1, 44, 44] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042986 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042986
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042986/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042986
Building REAL250005042987
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042987'
/scratch/stefan/7916125/working/building/REAL250005042987 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042987

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042987/0 /scratch/stefan/7916125/working/building/REAL250005042987 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/95
`/scratch/stefan/7916125/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042987 none C=CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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: [78, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 47, 47, 47, 47, 47, 1, 78, 78, 78, 38, 114, 6, 1, 1, 9, 9, 43, 47, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 475
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042987 none C=CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 123, 201, 123, 123, 47, 47, 47, 47, 14, 47, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 603, 123, 47, 47, 13, 13, 3, 1, 47, 47] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1354
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042987 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042987
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042987/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042987
Building REAL250005042988
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042988'
/scratch/stefan/7916125/working/building/REAL250005042988 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042988

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042988/0 /scratch/stefan/7916125/working/building/REAL250005042988 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/96
`/scratch/stefan/7916125/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042988 none CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
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: [48, 6, 48, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 58, 58, 58, 95, 95, 95, 95, 95, 1, 48, 48, 48, 48, 144, 6, 1, 1, 10, 10, 58, 95, 1, 1] 603
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 512
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042988 none CC(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 95, 95, 95, 95, 27, 95, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 603, 173, 95, 95, 27, 27, 6, 1, 95, 95] 603
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1273
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042988 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042988
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042988/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042988
Building REAL250005042989
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042989'
/scratch/stefan/7916125/working/building/REAL250005042989 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042989

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042989/0 /scratch/stefan/7916125/working/building/REAL250005042989 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/97
`/scratch/stefan/7916125/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042989 none CC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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]
0  hydrogens 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, 6, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 58, 58, 58, 88, 88, 88, 88, 88, 1, 37, 37, 37, 6, 1, 1, 10, 10, 58, 88, 1, 1] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 287
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042989 none CC(=O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 88, 88, 88, 88, 25, 88, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 173, 88, 88, 24, 24, 4, 1, 88, 88] 201
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 620
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042989 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042989
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042989/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042989
Building REAL250005042990
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042990'
/scratch/stefan/7916125/working/building/REAL250005042990 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042990

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042990/0 /scratch/stefan/7916125/working/building/REAL250005042990 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/98
`/scratch/stefan/7916125/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005042990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042990 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 51, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 46, 46, 46, 1, 51, 70, 70, 70, 70, 70, 51, 9, 9, 1, 1, 6, 46, 46, 46, 46, 1, 1, 70] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 16, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35])
total number of confs: 266
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042990 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 139, 46, 46, 46, 46, 10, 46, 10, 1, 10, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 201, 139, 139, 46, 46, 10, 1, 1, 1, 1, 46, 46, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 718
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042990 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 21, 70, 70, 70, 70, 70, 168, 168, 168, 201, 201, 201, 70, 1, 1, 1, 1, 1, 1, 3, 20, 20, 70, 70, 168, 201, 201, 201, 201, 70, 70, 1] 201
rigid atoms, others: [1, 35, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 610
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042990 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042990
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042990/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042990
Building REAL250005042991
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042991'
/scratch/stefan/7916125/working/building/REAL250005042991 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042991

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042991/0 /scratch/stefan/7916125/working/building/REAL250005042991 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/99
`/scratch/stefan/7916125/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042991 none CC=C(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 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: [42, 42, 6, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 52, 86, 86, 86, 86, 86, 1, 42, 42, 42, 42, 6, 1, 1, 9, 9, 52, 86, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 282
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042991 none CC=C(F)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 159, 201, 159, 159, 86, 86, 86, 86, 30, 86, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 159, 86, 86, 30, 30, 7, 1, 86, 86] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 639
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042991 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042991
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042991/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042991
Building REAL250005042992
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042992'
/scratch/stefan/7916125/working/building/REAL250005042992 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042992

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042992/0 /scratch/stefan/7916125/working/building/REAL250005042992 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/100
`/scratch/stefan/7916125/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042992 none CC(CO)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 35, 62, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 44, 44, 44, 47, 47, 47, 47, 47, 1, 35, 35, 35, 35, 62, 62, 186, 6, 1, 1, 9, 9, 44, 47, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 559
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042992 none CC(CO)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [200, 121, 200, 201, 121, 121, 47, 47, 47, 47, 12, 47, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 200, 200, 200, 200, 201, 201, 603, 121, 47, 47, 11, 11, 3, 1, 47, 47] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1345
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042992 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042992
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042992/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042992
Building REAL250005042993
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042993'
/scratch/stefan/7916125/working/building/REAL250005042993 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042993

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042993/0 /scratch/stefan/7916125/working/building/REAL250005042993 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/101
`/scratch/stefan/7916125/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005042993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042993 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 45, 45, 45, 1, 55, 74, 74, 74, 74, 74, 55, 10, 10, 1, 1, 6, 135, 45, 45, 45, 45, 1, 1, 74] 603
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 408
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042993 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 139, 45, 45, 45, 45, 11, 45, 11, 1, 11, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 139, 139, 45, 45, 11, 6, 1, 1, 1, 1, 45, 45, 201] 603
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 735
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: REAL250005042993 none O=C(NC[C@@H]1C[C@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 23, 74, 74, 74, 74, 74, 174, 174, 174, 201, 201, 201, 74, 1, 1, 1, 1, 1, 1, 4, 23, 23, 74, 74, 174, 603, 201, 201, 201, 201, 74, 74, 1] 603
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 1210
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042993 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042993
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042993/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042993
Building REAL250005042994
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042994'
/scratch/stefan/7916125/working/building/REAL250005042994 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042994

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042994/0 /scratch/stefan/7916125/working/building/REAL250005042994 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/102
`/scratch/stefan/7916125/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005042994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042994 none O=C(N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 57, 104, 104, 104, 104, 104, 1, 6, 31, 31, 31, 6, 1, 1, 10, 10, 57, 104, 1, 1, 31, 31, 31, 31, 31] 135
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 24, 25, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 263
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042994 none O=C(N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 104, 104, 104, 104, 39, 104, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 104, 135, 135, 135, 135, 135, 104, 104, 38, 38, 8, 1, 104, 104, 135, 135, 135, 135, 135] 135
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 423
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: REAL250005042994 none O=C(N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 31, 31, 31, 31, 31, 84, 127, 127, 127, 135, 135, 135, 135, 135, 31, 1, 1, 1, 1, 12, 31, 31, 84, 84, 127, 135, 31, 31, 1, 1, 1, 1, 1] 135
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 449
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042994 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042994
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042994/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042994
Building REAL250005042995
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042995'
/scratch/stefan/7916125/working/building/REAL250005042995 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042995

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042995/0 /scratch/stefan/7916125/working/building/REAL250005042995 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/103
`/scratch/stefan/7916125/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042995 none CC(CF)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 36, 68, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 44, 44, 44, 44, 44, 1, 36, 36, 36, 36, 68, 68, 6, 1, 1, 9, 9, 40, 44, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 391
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042995 none CC(CF)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 113, 199, 201, 113, 113, 44, 44, 44, 44, 12, 44, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 199, 199, 199, 199, 201, 201, 113, 44, 44, 12, 12, 4, 1, 44, 44] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042995 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042995
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042995/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042995
Building REAL250005042996
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042996'
/scratch/stefan/7916125/working/building/REAL250005042996 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042996

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042996/0 /scratch/stefan/7916125/working/building/REAL250005042996 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/104
`/scratch/stefan/7916125/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042996 none CC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [39, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 60, 60, 60, 108, 108, 108, 108, 108, 1, 39, 39, 39, 39, 39, 6, 1, 1, 10, 10, 60, 108, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 319
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042996 none CC=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 173, 173, 173, 108, 108, 108, 108, 36, 108, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 173, 108, 108, 35, 35, 7, 1, 108, 108] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 642
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042996 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042996
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042996/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042996
Building REAL250005042997
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042997'
/scratch/stefan/7916125/working/building/REAL250005042997 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042997

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042997/0 /scratch/stefan/7916125/working/building/REAL250005042997 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/105
`/scratch/stefan/7916125/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042997 none O=C(C=CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need 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, 30, 30, 83, 1, 1, 1, 1, 1, 1, 1, 8, 42, 42, 42, 44, 44, 44, 44, 44, 1, 30, 30, 83, 83, 6, 1, 1, 8, 8, 42, 44, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 395
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042997 none O=C(C=CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [123, 123, 123, 198, 198, 201, 44, 44, 44, 44, 12, 44, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 198, 198, 201, 201, 123, 44, 44, 11, 11, 3, 1, 44, 44] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 607
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042997 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042997
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042997/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042997
Building REAL250005042998
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042998'
/scratch/stefan/7916125/working/building/REAL250005042998 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005042998 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005042998' -> `/scratch/stefan/7916125/failed/REAL250005042998'
Building REAL250005042999
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005042999'
/scratch/stefan/7916125/working/building/REAL250005042999 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005042999

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005042999/0 /scratch/stefan/7916125/working/building/REAL250005042999 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/106
`/scratch/stefan/7916125/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005042999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005042999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005042999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042999 none C[C@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [46, 6, 46, 46, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 59, 59, 59, 96, 96, 96, 96, 96, 1, 46, 46, 46, 138, 6, 1, 1, 10, 10, 59, 96, 1, 1] 603
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 501
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005042999 none C[C@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 175, 201, 201, 175, 175, 96, 96, 96, 96, 27, 96, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 603, 175, 96, 96, 26, 26, 6, 1, 96, 96] 603
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1269
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005042999 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005042999
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005042999/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005042999
Building REAL250005043000
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043000'
/scratch/stefan/7916125/working/building/REAL250005043000 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043000

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043000/0 /scratch/stefan/7916125/working/building/REAL250005043000 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/107
`/scratch/stefan/7916125/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043000 none CON=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [51, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 59, 59, 59, 126, 126, 126, 126, 126, 1, 51, 51, 51, 27, 6, 1, 1, 9, 9, 59, 126, 1, 1] 200
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 353
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043000 none CON=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 199, 199, 199, 126, 126, 126, 126, 44, 126, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 126, 200, 200, 200, 200, 199, 126, 126, 44, 44, 9, 1, 126, 126] 200
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 634
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043000 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043000
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043000/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043000
Building REAL250005043001
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043001'
/scratch/stefan/7916125/working/building/REAL250005043001 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043001

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043001/0 /scratch/stefan/7916125/working/building/REAL250005043001 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/108
`/scratch/stefan/7916125/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043001 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 44, 44, 44, 44, 144, 201, 201, 201, 201, 201, 201, 201, 201, 44, 2, 2, 2, 1, 1, 12, 44, 44, 144, 144, 201, 201, 44, 44] 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])
total number of confs: 719
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043001 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [44, 44, 44, 44, 6, 44, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 65, 65, 65, 65, 65, 1, 44, 44, 44, 44, 44, 6, 1, 1, 9, 9, 48, 65, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
total number of confs: 253
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: REAL250005043001 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 128, 201, 128, 128, 65, 65, 65, 65, 20, 65, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 128, 65, 65, 20, 20, 4, 1, 65, 65] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 622
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043001 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043001
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043001/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043001
Building REAL250005043002
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043002'
/scratch/stefan/7916125/working/building/REAL250005043002 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043002

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043002/0 /scratch/stefan/7916125/working/building/REAL250005043002 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/109
`/scratch/stefan/7916125/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043002 none CC(C)(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 57, 57, 57, 86, 86, 86, 86, 86, 1, 36, 36, 36, 36, 36, 36, 108, 6, 1, 1, 9, 9, 57, 86, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 420
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043002 none CC(C)(O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 160, 201, 201, 160, 160, 86, 86, 86, 86, 25, 86, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 603, 160, 86, 86, 24, 24, 6, 1, 86, 86] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1305
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043002 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043002
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043002/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043002
Building REAL250005043003
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043003'
/scratch/stefan/7916125/working/building/REAL250005043003 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043003

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043003/0 /scratch/stefan/7916125/working/building/REAL250005043003 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/110
`/scratch/stefan/7916125/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043003 none C=C(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 43, 68, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 45, 45, 45, 45, 45, 1, 68, 68, 68, 68, 68, 43, 43, 6, 1, 1, 9, 9, 42, 45, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043003 none C=C(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 114, 114, 114, 45, 45, 45, 45, 12, 45, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 114, 45, 45, 11, 11, 3, 1, 45, 45] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043003 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043003
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043003/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043003
Building REAL250005043004
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043004'
/scratch/stefan/7916125/working/building/REAL250005043004 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043004

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043004/0 /scratch/stefan/7916125/working/building/REAL250005043004 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/111
`/scratch/stefan/7916125/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043004 none C=CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [76, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 50, 50, 50, 50, 50, 1, 76, 76, 76, 45, 45, 6, 1, 1, 9, 9, 47, 50, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 374
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043004 none C=CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 134, 134, 134, 50, 50, 50, 50, 13, 50, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 134, 50, 50, 13, 13, 4, 1, 50, 50] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 737
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043004 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043004
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043004/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043004
Building REAL250005043005
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043005'
/scratch/stefan/7916125/working/building/REAL250005043005 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043005

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043005/0 /scratch/stefan/7916125/working/building/REAL250005043005 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/112
`/scratch/stefan/7916125/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043005 none C[NH+](C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [17, 15, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 31, 31, 31, 31, 31, 1, 17, 17, 17, 17, 17, 17, 15, 15, 6, 1, 1, 4, 4, 14, 31, 1, 1] 42
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13, 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, 35, 36, 37, 38])
total number of confs: 125
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043005 none C[NH+](C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 41, 42, 42, 40, 40, 40, 31, 31, 31, 31, 19, 31, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 42, 42, 42, 42, 42, 42, 41, 41, 40, 31, 31, 19, 19, 8, 1, 31, 31] 42
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 154
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043005 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043005/1 /scratch/stefan/7916125/working/building/REAL250005043005 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/113
`/scratch/stefan/7916125/working/3D/113' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043005.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043005/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043005 none CN(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 38, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 58, 58, 58, 58, 58, 1, 54, 54, 54, 54, 54, 54, 38, 38, 6, 1, 1, 9, 9, 50, 58, 1, 1] 201
rigid atoms, others: [32, 33, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39] 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, 34, 35, 36, 37])
total number of confs: 323
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043005 none CN(C)CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 125, 125, 125, 58, 58, 58, 58, 17, 58, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 200, 200, 125, 58, 58, 17, 17, 4, 1, 58, 58] 201
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 742
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043005 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043005
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043005/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043005/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043005
Building REAL250005043006
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043006'
/scratch/stefan/7916125/working/building/REAL250005043006 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043006

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043006/0 /scratch/stefan/7916125/working/building/REAL250005043006 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/114
`/scratch/stefan/7916125/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043006 none N#CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 53, 66, 66, 66, 66, 66, 1, 56, 56, 6, 1, 1, 9, 9, 53, 66, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 21, 25, 26, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 335
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043006 none N#CCC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
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, 66, 66, 66, 66, 19, 66, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 66, 201, 201, 150, 66, 66, 18, 18, 4, 1, 66, 66] 201
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 705
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043006 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043006
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043006/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043006
Building REAL250005043007
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043007'
/scratch/stefan/7916125/working/building/REAL250005043007 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043007

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043007/0 /scratch/stefan/7916125/working/building/REAL250005043007 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/115
`/scratch/stefan/7916125/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1)

`REAL250005043007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043007 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 44, 1, 44, 67, 67, 67, 67, 67, 44, 8, 8, 1, 1, 6, 44, 44, 44, 44, 1, 1, 67] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 16, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35])
total number of confs: 254
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043007 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 120, 44, 44, 44, 44, 11, 44, 11, 1, 11, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 201, 201, 120, 120, 44, 44, 11, 1, 1, 1, 1, 44, 44, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 699
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043007 none O=C(NC[C@@H]1C[C@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 24, 67, 67, 67, 67, 67, 141, 141, 141, 201, 201, 201, 67, 1, 1, 1, 1, 1, 1, 4, 24, 24, 67, 67, 141, 201, 201, 201, 201, 67, 67, 1] 201
rigid atoms, others: [1, 35, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 618
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043007 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043007
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043007/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043007
Building REAL250005043008
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043008'
/scratch/stefan/7916125/working/building/REAL250005043008 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043008

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043008/0 /scratch/stefan/7916125/working/building/REAL250005043008 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/116
`/scratch/stefan/7916125/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043008 none O=C(CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens need 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, 42, 63, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 42, 47, 47, 47, 47, 47, 1, 42, 42, 63, 63, 6, 1, 1, 9, 9, 42, 47, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 379
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043008 none O=C(CCF)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 201, 201, 47, 47, 47, 47, 14, 47, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 113, 47, 47, 14, 14, 4, 1, 47, 47] 201
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 745
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043008 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043008
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043008/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043008
Building REAL250005043009
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043009'
/scratch/stefan/7916125/working/building/REAL250005043009 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043009

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043009/0 /scratch/stefan/7916125/working/building/REAL250005043009 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/117
`/scratch/stefan/7916125/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043009 none CO[C@H](C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 6, 40, 40, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 63, 63, 63, 63, 63, 1, 53, 53, 53, 40, 40, 40, 6, 1, 1, 9, 9, 50, 63, 1, 1] 201
rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 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, 33, 34, 35, 36])
total number of confs: 306
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043009 none CO[C@H](C)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 201, 139, 139, 63, 63, 63, 63, 20, 63, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 139, 63, 63, 20, 20, 4, 1, 63, 63] 201
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 715
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043009 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043009
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043009/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043009
Building REAL250005043010
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043010'
/scratch/stefan/7916125/working/building/REAL250005043010 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043010

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043010/0 /scratch/stefan/7916125/working/building/REAL250005043010 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/118
`/scratch/stefan/7916125/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043010 none C[C@@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 6, 45, 45, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 57, 87, 87, 87, 87, 87, 1, 45, 45, 45, 135, 6, 1, 1, 10, 10, 57, 87, 1, 1] 603
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 479
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043010 none C[C@@H](O)C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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, 172, 201, 201, 172, 172, 87, 87, 87, 87, 27, 87, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 603, 172, 87, 87, 26, 26, 5, 1, 87, 87] 603
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1292
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043010 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043010
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043010/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043010
Building REAL250005043011
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043011'
/scratch/stefan/7916125/working/building/REAL250005043011 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043011

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043011/0 /scratch/stefan/7916125/working/building/REAL250005043011 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/119
`/scratch/stefan/7916125/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043011 none C=C1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 12, 12, 12, 49, 49, 49, 49, 49, 153, 201, 201, 201, 201, 201, 201, 201, 201, 49, 1, 1, 1, 1, 1, 12, 49, 49, 153, 153, 201, 201, 49, 49] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 734
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043011 none C=C1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [49, 49, 49, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 54, 54, 54, 54, 54, 1, 49, 49, 49, 49, 49, 6, 1, 1, 9, 9, 48, 54, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 242
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: REAL250005043011 none C=C1CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 126, 126, 126, 54, 54, 54, 54, 15, 54, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 126, 54, 54, 15, 15, 4, 1, 54, 54] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 615
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043011 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043011
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043011/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043011
Building REAL250005043012
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043012'
/scratch/stefan/7916125/working/building/REAL250005043012 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043012

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043012/0 /scratch/stefan/7916125/working/building/REAL250005043012 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/120
`/scratch/stefan/7916125/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043012 none CC1=CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 54, 54, 54, 54, 54, 141, 201, 201, 201, 201, 201, 201, 201, 201, 54, 2, 2, 2, 1, 1, 13, 54, 54, 141, 141, 201, 201, 54, 54] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 739
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043012 none CC1=CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [54, 54, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 60, 60, 60, 60, 60, 1, 54, 54, 54, 54, 54, 6, 1, 1, 9, 9, 49, 60, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 264
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: REAL250005043012 none CC1=CC1C(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 141, 141, 141, 60, 60, 60, 60, 15, 60, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 141, 60, 60, 15, 15, 3, 1, 60, 60] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 604
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043012 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043012
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043012/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043012
Building REAL250005043013
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043013'
/scratch/stefan/7916125/working/building/REAL250005043013 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043013

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043013/0 /scratch/stefan/7916125/working/building/REAL250005043013 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/121
`/scratch/stefan/7916125/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043013 none C=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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]
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: [33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 58, 58, 58, 123, 123, 123, 123, 123, 1, 33, 33, 33, 6, 1, 1, 10, 10, 58, 123, 1, 1] 192
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 319
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043013 none C=CC(=O)N[C@H]1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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]
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, 123, 123, 123, 123, 50, 123, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 123, 192, 192, 192, 192, 123, 123, 50, 50, 9, 1, 123, 123] 192
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 609
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043013 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043013
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043013/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043013
Building REAL250005043014
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043014'
/scratch/stefan/7916125/working/building/REAL250005043014 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043014

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043014/0 /scratch/stefan/7916125/working/building/REAL250005043014 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/122
`/scratch/stefan/7916125/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043014 none CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [144, 54, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 144, 144, 144, 144, 144, 54, 10, 10, 1, 1, 6, 28, 1, 1] 196
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 566
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043014 none CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [196, 167, 167, 167, 98, 28, 28, 28, 28, 9, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 196, 196, 196, 196, 196, 167, 98, 98, 28, 28, 9, 1, 28, 28] 196
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 739
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043014 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043014
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043014/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043014
Building REAL250005043015
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043015'
/scratch/stefan/7916125/working/building/REAL250005043015 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043015

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043015/0 /scratch/stefan/7916125/working/building/REAL250005043015 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/123
`/scratch/stefan/7916125/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043015 none COCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [163, 134, 123, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 163, 163, 163, 134, 134, 123, 123, 34, 7, 7, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 568
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043015 none COCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 126, 126, 126, 43, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 200, 200, 126, 43, 43, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 730
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043015 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043015
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043015/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043015
Building REAL250005043016
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043016'
/scratch/stefan/7916125/working/building/REAL250005043016 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043016

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043016/0 /scratch/stefan/7916125/working/building/REAL250005043016 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/124
`/scratch/stefan/7916125/working/3D/124' -> `0.mol2'
Preparing input files

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

`REAL250005043016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043016 none CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 36, 36, 36, 36, 10, 10, 1, 1, 6, 20, 1, 1] 57
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 19, 26, 27, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29])
total number of confs: 128
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043016 none CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 51, 20, 20, 20, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 57, 57, 57, 57, 51, 51, 20, 20, 9, 1, 20, 20] 57
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043016 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043016
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043016/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043016
Building REAL250005043017
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043017'
/scratch/stefan/7916125/working/building/REAL250005043017 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043017

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043017/0 /scratch/stefan/7916125/working/building/REAL250005043017 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/125
`/scratch/stefan/7916125/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1)

`REAL250005043017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043017 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 46, 137, 137, 46, 10, 10, 1, 1, 6, 22, 1, 1, 137, 137, 137, 137, 137] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 25, 26, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35])
total number of confs: 398
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043017 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 78, 22, 22, 22, 22, 6, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 140, 201, 201, 140, 78, 78, 22, 22, 6, 1, 22, 22, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 684
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043017 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 68, 137, 137, 137, 137, 137, 195, 195, 195, 201, 201, 201, 201, 201, 137, 1, 1, 1, 13, 68, 68, 137, 137, 195, 201, 137, 137, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 660
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043017 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043017
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043017/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043017
Building REAL250005043018
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043018'
/scratch/stefan/7916125/working/building/REAL250005043018 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043018

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043018/0 /scratch/stefan/7916125/working/building/REAL250005043018 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/126
`/scratch/stefan/7916125/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1)

`REAL250005043018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043018 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 46, 140, 140, 140, 46, 10, 10, 1, 1, 6, 19, 1, 1, 140, 140, 140, 140, 140, 140, 140] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 413
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043018 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 71, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 132, 201, 201, 201, 132, 71, 71, 19, 19, 5, 1, 19, 19, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 660
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: REAL250005043018 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 61, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 201, 140, 1, 1, 1, 1, 13, 61, 61, 140, 140, 201, 201, 140, 140, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 651
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043018 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043018
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043018/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043018
Building REAL250005043019
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043019'
/scratch/stefan/7916125/working/building/REAL250005043019 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043019

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043019/0 /scratch/stefan/7916125/working/building/REAL250005043019 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/127
`/scratch/stefan/7916125/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043019 none O=C(CC1CC1)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 3, 1, 1, 1, 1, 21, 21, 109, 174, 174, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 174, 3, 3, 1, 1, 1, 1, 1, 21, 109, 109, 174, 174, 201, 201, 174, 174] 201
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])
total number of confs: 716
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043019 none O=C(CC1CC1)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 37, 37, 145, 174, 174, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 145, 145, 174, 174, 174, 174, 174, 37, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 658
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043019 none O=C(CC1CC1)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 113, 113, 188, 201, 201, 43, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 188, 188, 201, 201, 201, 201, 201, 113, 43, 43, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 758
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043019 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043019
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043019/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043019
Building REAL250005043020
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043020'
/scratch/stefan/7916125/working/building/REAL250005043020 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043020

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043020/0 /scratch/stefan/7916125/working/building/REAL250005043020 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/128
`/scratch/stefan/7916125/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043020 none CC(C)(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 135, 135, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 135, 135, 135, 135, 135, 135, 46, 8, 8, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 524
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043020 none CC(C)(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 146, 201, 201, 146, 146, 60, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 146, 60, 60, 20, 20, 6, 1, 20, 20] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 752
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043020 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043020
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043020/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043020
Building REAL250005043021
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043021'
/scratch/stefan/7916125/working/building/REAL250005043021 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043021

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043021/0 /scratch/stefan/7916125/working/building/REAL250005043021 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/129
`/scratch/stefan/7916125/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043021 none COCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [123, 106, 42, 42, 42, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 123, 123, 123, 109, 109, 42, 7, 7, 1, 1, 6, 27, 1, 1] 190
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 470
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043021 none COCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [190, 190, 166, 166, 166, 81, 27, 27, 27, 27, 6, 27, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 190, 190, 190, 190, 190, 166, 81, 81, 27, 27, 6, 1, 27, 27] 190
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 669
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043021 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043021
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043021/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043021
Building REAL250005043022
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043022'
/scratch/stefan/7916125/working/building/REAL250005043022 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043022

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043022/0 /scratch/stefan/7916125/working/building/REAL250005043022 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/130
`/scratch/stefan/7916125/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043022 none CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 133, 41, 41, 41, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 157, 157, 157, 157, 157, 133, 133, 41, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 659
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043022 none CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 125, 125, 125, 45, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 195, 195, 125, 45, 45, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 773
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043022 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043022
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043022/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043022
Building REAL250005043023
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043023'
/scratch/stefan/7916125/working/building/REAL250005043023 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043023

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043023/0 /scratch/stefan/7916125/working/building/REAL250005043023 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/131
`/scratch/stefan/7916125/working/3D/131' -> `0.mol2'
Preparing input files

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

`REAL250005043023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043023 none CC(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 133, 150, 48, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 150, 150, 150, 150, 150, 150, 150, 133, 133, 48, 8, 8, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 694
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043023 none CC(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [197, 200, 201, 122, 122, 122, 57, 14, 14, 14, 14, 5, 14, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 201, 201, 200, 200, 122, 57, 57, 14, 14, 5, 1, 14, 14] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 806
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043023 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043023
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043023/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043023
Building REAL250005043024
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043024'
/scratch/stefan/7916125/working/building/REAL250005043024 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043024

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043024/0 /scratch/stefan/7916125/working/building/REAL250005043024 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/132
`/scratch/stefan/7916125/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043024 none CC1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 70, 146, 146, 146, 146, 146, 200, 200, 200, 201, 201, 201, 201, 201, 146, 2, 2, 2, 1, 1, 1, 1, 12, 70, 70, 146, 146, 200, 201, 146, 146] 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])
total number of confs: 664
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043024 none CC1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 48, 48, 48, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 146, 146, 146, 146, 146, 146, 146, 48, 9, 9, 1, 1, 6, 19, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 422
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043024 none CC1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 64, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 127, 64, 64, 19, 19, 6, 1, 19, 19] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 645
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043024 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043024
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043024/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043024
Building REAL250005043025
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043025'
/scratch/stefan/7916125/working/building/REAL250005043025 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043025

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043025/0 /scratch/stefan/7916125/working/building/REAL250005043025 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/133
`/scratch/stefan/7916125/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043025 none CCOCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 157, 94, 40, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 159, 159, 159, 159, 159, 100, 100, 40, 7, 7, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043025 none CCOCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 179, 120, 120, 120, 42, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 183, 183, 120, 42, 42, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043025 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043025
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043025/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043025
Building REAL250005043026
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043026'
/scratch/stefan/7916125/working/building/REAL250005043026 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043026

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043026/0 /scratch/stefan/7916125/working/building/REAL250005043026 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/134
`/scratch/stefan/7916125/working/3D/134' -> `0.mol2'
Preparing input files

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

`REAL250005043026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043026 none CC(C)=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 140, 59, 59, 59, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 140, 140, 140, 140, 140, 140, 140, 59, 10, 10, 1, 1, 6, 26, 1, 1] 197
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 436
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043026 none CC(C)=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 197, 167, 167, 167, 95, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 197, 197, 197, 197, 197, 197, 197, 167, 95, 95, 26, 26, 8, 1, 26, 26] 197
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 670
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043026 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043026
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043026/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043026
Building REAL250005043027
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043027'
/scratch/stefan/7916125/working/building/REAL250005043027 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043027

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043027/0 /scratch/stefan/7916125/working/building/REAL250005043027 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/135
`/scratch/stefan/7916125/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043027 none CSCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [161, 117, 41, 41, 41, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 161, 161, 161, 117, 117, 41, 7, 7, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 515
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043027 none CSCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 181, 113, 113, 113, 49, 14, 14, 14, 14, 3, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 181, 181, 113, 49, 49, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 719
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043027 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043027
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043027/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043027
Building REAL250005043028
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043028'
/scratch/stefan/7916125/working/building/REAL250005043028 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043028

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043028/0 /scratch/stefan/7916125/working/building/REAL250005043028 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/136
`/scratch/stefan/7916125/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043028 none CCCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 137, 123, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 157, 159, 159, 159, 159, 149, 149, 123, 123, 31, 7, 7, 1, 1, 6, 8, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 728
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043028 none CCCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [199, 199, 187, 85, 85, 85, 27, 8, 8, 8, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 199, 201, 201, 201, 201, 199, 199, 187, 187, 85, 27, 27, 8, 8, 4, 1, 8, 8] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043028 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043028
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043028/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043028
Building REAL250005043029
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043029'
/scratch/stefan/7916125/working/building/REAL250005043029 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043029

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043029/0 /scratch/stefan/7916125/working/building/REAL250005043029 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/137
`/scratch/stefan/7916125/working/3D/137' -> `0.mol2'
Preparing input files

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

`REAL250005043029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043029 none CC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [126, 50, 126, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 126, 126, 126, 126, 126, 126, 126, 50, 10, 10, 1, 1, 6, 27, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 512
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043029 none CC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 171, 201, 171, 171, 93, 27, 27, 27, 27, 8, 27, 8, 1, 8, 1, 1, 1, 1, 1, 1, 27, 201, 201, 201, 201, 201, 201, 201, 171, 93, 93, 27, 27, 8, 1, 27, 27] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043029 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043029
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043029/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043029
Building REAL250005043030
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043030'
/scratch/stefan/7916125/working/building/REAL250005043030 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043030

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043030/0 /scratch/stefan/7916125/working/building/REAL250005043030 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/138
`/scratch/stefan/7916125/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043030 none CCC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [151, 131, 43, 131, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 155, 155, 155, 155, 155, 131, 131, 131, 131, 43, 8, 8, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043030 none CCC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 129, 198, 129, 129, 50, 13, 13, 13, 13, 4, 13, 3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 198, 198, 198, 198, 129, 50, 50, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043030 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043030
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043030/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043030
Building REAL250005043031
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043031'
/scratch/stefan/7916125/working/building/REAL250005043031 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043031

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043031/0 /scratch/stefan/7916125/working/building/REAL250005043031 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/139
`/scratch/stefan/7916125/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043031 none COC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 121, 49, 129, 49, 49, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 150, 150, 150, 129, 129, 129, 129, 49, 8, 8, 1, 1, 6, 25, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 558
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043031 none COC(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 161, 201, 161, 161, 72, 25, 25, 25, 25, 7, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 25, 201, 201, 201, 201, 201, 201, 201, 161, 72, 72, 25, 25, 7, 1, 25, 25] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 731
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043031 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043031
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043031/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043031
Building REAL250005043032
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043032'
/scratch/stefan/7916125/working/building/REAL250005043032 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043032

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043032/0 /scratch/stefan/7916125/working/building/REAL250005043032 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/140
`/scratch/stefan/7916125/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043032 none C=CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [173, 131, 111, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 173, 173, 173, 131, 131, 111, 111, 23, 7, 7, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 692
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043032 none C=CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 185, 93, 93, 93, 38, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 185, 185, 93, 38, 38, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 817
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043032 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043032
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043032/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043032
Building REAL250005043033
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043033'
/scratch/stefan/7916125/working/building/REAL250005043033 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043033

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043033/0 /scratch/stefan/7916125/working/building/REAL250005043033 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/141
`/scratch/stefan/7916125/working/3D/141' -> `0.mol2'
Preparing input files

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

`REAL250005043033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043033 none CC=C(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 50, 155, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 155, 155, 155, 155, 155, 155, 155, 50, 10, 10, 1, 1, 6, 19, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 441
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043033 none CC=C(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 201, 157, 157, 68, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 201, 201, 157, 68, 68, 19, 19, 5, 1, 19, 19] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 658
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043033 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043033
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043033/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043033
Building REAL250005043034
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043034'
/scratch/stefan/7916125/working/building/REAL250005043034 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043034

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043034/0 /scratch/stefan/7916125/working/building/REAL250005043034 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/142
`/scratch/stefan/7916125/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC[C@H]2C[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005043034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043034 none CC1(C(=O)NC[C@H]2C[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 7, 7, 47, 146, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 146, 1, 1, 2, 2, 2, 7, 47, 47, 146, 146, 201, 201, 146, 146, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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])
total number of confs: 633
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043034 none CC1(C(=O)NC[C@H]2C[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [146, 45, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 146, 146, 146, 146, 146, 45, 10, 10, 1, 1, 6, 16, 1, 1, 146, 146, 146, 146] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 20, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 35, 36, 37, 38])
total number of confs: 420
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043034 none CC1(C(=O)NC[C@H]2C[C@H](NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 127, 127, 127, 63, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 127, 63, 63, 16, 16, 3, 1, 16, 16, 201, 201, 201, 201] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043034 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043034
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043034/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043034
Building REAL250005043035
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043035'
/scratch/stefan/7916125/working/building/REAL250005043035 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043035

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043035/0 /scratch/stefan/7916125/working/building/REAL250005043035 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/143
`/scratch/stefan/7916125/working/3D/143' -> `0.mol2'
Preparing input files

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

`REAL250005043035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043035 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 146, 146, 146, 146, 146, 200, 200, 200, 201, 201, 201, 201, 201, 146, 2, 2, 2, 1, 1, 12, 69, 69, 146, 146, 200, 201, 146, 146] 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])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043035 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [146, 146, 146, 146, 50, 146, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 146, 146, 146, 146, 146, 50, 9, 9, 1, 1, 6, 19, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043035 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 130, 201, 130, 130, 62, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 130, 62, 62, 19, 19, 5, 1, 19, 19] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043035 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043035
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043035/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043035
Building REAL250005043036
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043036'
/scratch/stefan/7916125/working/building/REAL250005043036 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043036

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043036/0 /scratch/stefan/7916125/working/building/REAL250005043036 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/144
`/scratch/stefan/7916125/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043036 none CCC(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 131, 43, 131, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 158, 158, 158, 158, 158, 131, 43, 8, 8, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 736
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043036 none CCC(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 127, 195, 127, 127, 46, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 195, 127, 46, 46, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 748
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043036 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043036
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043036/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043036
Building REAL250005043037
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043037'
/scratch/stefan/7916125/working/building/REAL250005043037 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043037

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043037/0 /scratch/stefan/7916125/working/building/REAL250005043037 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/145
`/scratch/stefan/7916125/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043037 none O=C(CCCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 116, 109, 167, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 116, 116, 137, 137, 154, 154, 29, 7, 7, 1, 1, 6, 8, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 830
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043037 none O=C(CCCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 190, 197, 201, 25, 8, 8, 8, 8, 3, 8, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 190, 190, 201, 201, 201, 201, 85, 25, 25, 8, 8, 3, 1, 8, 8] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 787
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043037 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043037
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043037/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043037
Building REAL250005043038
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043038'
/scratch/stefan/7916125/working/building/REAL250005043038 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043038

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043038/0 /scratch/stefan/7916125/working/building/REAL250005043038 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/146
`/scratch/stefan/7916125/working/3D/146' -> `0.mol2'
Preparing input files

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

`REAL250005043038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043038 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 149, 149, 149, 149, 149, 200, 200, 200, 201, 201, 201, 201, 201, 149, 2, 2, 2, 1, 1, 12, 69, 69, 149, 149, 200, 201, 149, 149] 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])
total number of confs: 667
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043038 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [149, 149, 149, 149, 48, 149, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 149, 149, 149, 149, 149, 48, 8, 8, 1, 1, 6, 19, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 427
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043038 none C[C@H]1C[C@@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 127, 201, 127, 127, 64, 19, 19, 19, 19, 6, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 127, 64, 64, 19, 19, 6, 1, 19, 19] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 645
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043038 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043038
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043038/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043038
Building REAL250005043039
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043039'
/scratch/stefan/7916125/working/building/REAL250005043039 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043039

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043039/0 /scratch/stefan/7916125/working/building/REAL250005043039 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/147
`/scratch/stefan/7916125/working/3D/147' -> `0.mol2'
Preparing input files

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

`REAL250005043039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043039 none NC(=O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [86, 48, 86, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 1, 86, 86, 48, 10, 10, 1, 1, 6, 30, 1, 1] 148
rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 21, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043039 none NC(=O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
148  conformations in input
total number of sets (complete confs): 148
using faster count positions algorithm for large data
unique positions, atoms: [148, 142, 148, 142, 142, 82, 30, 30, 30, 30, 9, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 148, 148, 142, 82, 82, 30, 30, 9, 1, 30, 30] 148
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 502
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043039 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043039
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043039/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043039
Building REAL250005043040
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043040'
/scratch/stefan/7916125/working/building/REAL250005043040 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043040

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043040/0 /scratch/stefan/7916125/working/building/REAL250005043040 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/148
`/scratch/stefan/7916125/working/3D/148' -> `0.mol2'
Preparing input files

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

`REAL250005043040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043040 none CC(C)(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [65, 45, 65, 65, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 45, 9, 9, 1, 1, 6, 19, 1, 1] 97
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 255
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043040 none CC(C)(C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 87, 97, 97, 87, 87, 57, 19, 19, 19, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 97, 97, 97, 97, 97, 97, 97, 97, 97, 87, 57, 57, 19, 19, 7, 1, 19, 19] 97
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 364
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043040 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043040
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043040/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043040
Building REAL250005043041
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043041'
/scratch/stefan/7916125/working/building/REAL250005043041 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043041

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043041/0 /scratch/stefan/7916125/working/building/REAL250005043041 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/149
`/scratch/stefan/7916125/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043041 none C=CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [165, 107, 31, 31, 31, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 165, 165, 165, 107, 107, 31, 7, 7, 1, 1, 6, 26, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 613
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043041 none C=CCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 147, 147, 147, 71, 26, 26, 26, 26, 6, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 147, 71, 71, 26, 26, 7, 1, 26, 26] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043041 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043041
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043041/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043041
Building REAL250005043042
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043042'
/scratch/stefan/7916125/working/building/REAL250005043042 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043042

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043042/0 /scratch/stefan/7916125/working/building/REAL250005043042 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/150
`/scratch/stefan/7916125/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043042 none C[NH+](C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 87, 87, 47, 47, 47, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 87, 87, 87, 87, 87, 87, 87, 87, 47, 7, 7, 1, 1, 6, 20, 1, 1] 126
rigid atoms, others: [35, 36, 39, 8, 9, 10, 11, 12, 13, 14, 40, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38])
total number of confs: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043042 none C[NH+](C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 126, 108, 108, 108, 51, 20, 20, 20, 20, 7, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 126, 126, 126, 126, 126, 126, 126, 126, 108, 51, 51, 20, 20, 8, 1, 20, 20] 126
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 442
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043042 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043042/1 /scratch/stefan/7916125/working/building/REAL250005043042 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/151
`/scratch/stefan/7916125/working/3D/151' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043042.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043042/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043042 none CN(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [132, 116, 132, 54, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 132, 132, 132, 132, 132, 132, 116, 116, 54, 10, 10, 1, 1, 6, 27, 1, 1] 199
rigid atoms, others: [34, 35, 38, 7, 8, 9, 10, 11, 12, 13, 22, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 521
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043042 none CN(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
199  conformations in input
total number of sets (complete confs): 199
using faster count positions algorithm for large data
unique positions, atoms: [199, 199, 199, 161, 161, 161, 92, 27, 27, 27, 27, 9, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 199, 199, 199, 199, 199, 199, 199, 199, 161, 92, 92, 27, 27, 9, 1, 27, 27] 199
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 751
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043042 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043042
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043042/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043042/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043042
Building REAL250005043043
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043043'
/scratch/stefan/7916125/working/building/REAL250005043043 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043043

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043043/0 /scratch/stefan/7916125/working/building/REAL250005043043 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/152
`/scratch/stefan/7916125/working/3D/152' -> `0.mol2'
Preparing input files

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

`REAL250005043043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043043 none C=CC(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
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: [163, 99, 42, 99, 42, 42, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 1, 163, 163, 163, 99, 297, 42, 7, 7, 1, 1, 6, 21, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043043 none C=CC(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 201, 157, 157, 67, 21, 21, 21, 21, 5, 21, 5, 1, 5, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 603, 157, 67, 67, 21, 21, 5, 1, 21, 21] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1349
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043043 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043043
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043043/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043043
Building REAL250005043044
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043044'
/scratch/stefan/7916125/working/building/REAL250005043044 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043044

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043044/0 /scratch/stefan/7916125/working/building/REAL250005043044 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/153
`/scratch/stefan/7916125/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1)

`REAL250005043044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043044 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [47, 47, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 47, 149, 149, 149, 47, 9, 9, 1, 1, 6, 22, 1, 1, 149, 149, 149, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 429
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043044 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [130, 130, 74, 22, 22, 22, 22, 6, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 130, 201, 201, 201, 130, 74, 74, 22, 22, 6, 1, 22, 22, 201, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 680
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: REAL250005043044 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1COC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [13, 1, 13, 13, 61, 149, 149, 149, 149, 149, 199, 199, 199, 201, 201, 201, 201, 201, 149, 1, 1, 1, 1, 13, 61, 61, 149, 149, 199, 201, 149, 149, 1, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 661
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043044 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043044
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043044/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043044
Building REAL250005043045
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043045'
/scratch/stefan/7916125/working/building/REAL250005043045 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043045

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043045/0 /scratch/stefan/7916125/working/building/REAL250005043045 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/154
`/scratch/stefan/7916125/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043045 none CO[C@H](C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 121, 49, 129, 129, 49, 49, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 150, 150, 150, 129, 129, 129, 49, 8, 8, 1, 1, 6, 25, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 8, 9, 10, 11, 12, 13, 14, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 558
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043045 none CO[C@H](C)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 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', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 161, 201, 201, 161, 161, 72, 25, 25, 25, 25, 6, 25, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 201, 201, 201, 201, 201, 201, 161, 72, 72, 25, 25, 6, 1, 25, 25] 201
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043045 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043045
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043045/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043045
Building REAL250005043046
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043046'
/scratch/stefan/7916125/working/building/REAL250005043046 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043046

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043046/0 /scratch/stefan/7916125/working/building/REAL250005043046 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/155
`/scratch/stefan/7916125/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043046 none CCC=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 116, 116, 39, 39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 159, 159, 159, 159, 159, 116, 116, 39, 7, 7, 1, 1, 6, 16, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 595
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043046 none CCC=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 175, 175, 129, 129, 129, 57, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 201, 201, 201, 201, 201, 175, 175, 129, 57, 57, 16, 16, 4, 1, 16, 16] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043046 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043046
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043046/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043046
Building REAL250005043047
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043047'
/scratch/stefan/7916125/working/building/REAL250005043047 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005043047 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005043047' -> `/scratch/stefan/7916125/failed/REAL250005043047'
Building REAL250005043048
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043048'
/scratch/stefan/7916125/working/building/REAL250005043048 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043048

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043048/0 /scratch/stefan/7916125/working/building/REAL250005043048 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/156
`/scratch/stefan/7916125/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043048 none O=C(CO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
390  conformations in input
total number of sets (complete confs): 390
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 46, 97, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 27, 27, 27, 1, 97, 97, 291, 46, 10, 10, 1, 1, 6, 27, 1, 1] 390
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 20, 27, 28, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30])
total number of confs: 680
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043048 none O=C(CO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
390  conformations in input
total number of sets (complete confs): 390
using faster count positions algorithm for large data
unique positions, atoms: [126, 126, 126, 130, 80, 27, 27, 27, 27, 9, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 130, 130, 390, 126, 80, 80, 27, 27, 9, 1, 27, 27] 390
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 825
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043048 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043048
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043048/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043048
Building REAL250005043049
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043049'
/scratch/stefan/7916125/working/building/REAL250005043049 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043049

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043049/0 /scratch/stefan/7916125/working/building/REAL250005043049 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/157
`/scratch/stefan/7916125/working/3D/157' -> `0.mol2'
Preparing input files

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

`REAL250005043049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043049 none CC(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
573  conformations in input
total number of sets (complete confs): 573
using faster count positions algorithm for large data
unique positions, atoms: [141, 48, 137, 48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 1, 141, 141, 141, 141, 423, 48, 10, 10, 1, 1, 6, 30, 1, 1] 573
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 975
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043049 none CC(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
573  conformations in input
total number of sets (complete confs): 573
using faster count positions algorithm for large data
unique positions, atoms: [191, 164, 190, 164, 164, 92, 30, 30, 30, 30, 9, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 191, 191, 191, 191, 573, 164, 92, 92, 30, 30, 9, 1, 30, 30] 573
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1271
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043049 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043049
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043049/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043049
Building REAL250005043050
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043050'
/scratch/stefan/7916125/working/building/REAL250005043050 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043050

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043050/0 /scratch/stefan/7916125/working/building/REAL250005043050 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/158
`/scratch/stefan/7916125/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F)

`REAL250005043050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043050 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 48, 147, 147, 147, 48, 10, 10, 1, 1, 6, 18, 1, 1, 147, 147, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 426
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043050 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 70, 18, 18, 18, 18, 5, 18, 5, 1, 5, 1, 1, 1, 1, 1, 1, 18, 143, 201, 201, 201, 143, 70, 70, 18, 18, 5, 1, 18, 18, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 658
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043050 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CC1F NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 1, 13, 13, 66, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 1, 1, 1, 1, 13, 66, 66, 147, 147, 201, 201, 147, 147, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 661
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043050 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043050
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043050/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043050
Building REAL250005043051
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043051'
/scratch/stefan/7916125/working/building/REAL250005043051 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043051

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043051/0 /scratch/stefan/7916125/working/building/REAL250005043051 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/159
`/scratch/stefan/7916125/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043051 none O=C(CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens 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, 143, 153, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 143, 143, 153, 153, 35, 7, 7, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043051 none O=C(CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 109, 109, 201, 201, 37, 10, 10, 10, 10, 3, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 109, 37, 37, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 782
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043051 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043051
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043051/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043051
Building REAL250005043052
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043052'
/scratch/stefan/7916125/working/building/REAL250005043052 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043052

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043052/0 /scratch/stefan/7916125/working/building/REAL250005043052 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/160
`/scratch/stefan/7916125/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043052 none O=C(C=CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 109, 109, 168, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 109, 109, 168, 168, 42, 7, 7, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 621
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043052 none O=C(C=CCF)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 151, 195, 195, 201, 58, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 195, 195, 201, 201, 151, 58, 58, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 663
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043052 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043052
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043052/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043052
Building REAL250005043053
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043053'
/scratch/stefan/7916125/working/building/REAL250005043053 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043053

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043053/0 /scratch/stefan/7916125/working/building/REAL250005043053 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/161
`/scratch/stefan/7916125/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043053 none C#CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [159, 159, 139, 39, 39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 159, 159, 159, 139, 139, 39, 7, 7, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 616
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043053 none C#CCCC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 189, 111, 111, 111, 35, 10, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 189, 189, 111, 35, 35, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043053 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043053
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043053/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043053
Building REAL250005043054
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043054'
/scratch/stefan/7916125/working/building/REAL250005043054 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043054

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043054/0 /scratch/stefan/7916125/working/building/REAL250005043054 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/162
`/scratch/stefan/7916125/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1)

`REAL250005043054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043054 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 52, 116, 116, 116, 52, 10, 10, 1, 1, 6, 28, 1, 1, 116, 116, 116, 116, 116] 170
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 362
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043054 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 90, 28, 28, 28, 28, 8, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 146, 170, 170, 170, 146, 90, 90, 28, 28, 9, 1, 28, 28, 170, 170, 170, 170, 170] 170
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 579
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043054 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1CCO1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 61, 116, 116, 116, 116, 116, 161, 161, 161, 170, 170, 170, 170, 170, 116, 1, 1, 1, 1, 10, 61, 61, 116, 116, 161, 170, 116, 116, 1, 1, 1, 1, 1] 170
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 547
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043054 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043054
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043054/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043054
Building REAL250005043055
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043055'
/scratch/stefan/7916125/working/building/REAL250005043055 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043055

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043055/0 /scratch/stefan/7916125/working/building/REAL250005043055 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/163
`/scratch/stefan/7916125/working/3D/163' -> `0.mol2'
Preparing input files

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

`REAL250005043055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043055 none CC(C)(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [131, 51, 131, 127, 51, 51, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 131, 131, 131, 131, 131, 131, 393, 51, 9, 9, 1, 1, 6, 26, 1, 1] 603
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043055 none CC(C)(O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 161, 201, 199, 161, 161, 75, 26, 26, 26, 26, 6, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 201, 603, 161, 75, 75, 26, 26, 6, 1, 26, 26] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043055 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043055
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043055/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043055
Building REAL250005043056
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043056'
/scratch/stefan/7916125/working/building/REAL250005043056 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043056

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043056/0 /scratch/stefan/7916125/working/building/REAL250005043056 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/164
`/scratch/stefan/7916125/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043056 none CC1=CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 75, 166, 166, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 2, 2, 2, 1, 1, 13, 75, 75, 166, 166, 201, 201, 166, 166] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 679
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043056 none CC1=CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [166, 166, 166, 44, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 166, 166, 166, 166, 166, 44, 8, 8, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 456
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043056 none CC1=CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 123, 123, 123, 49, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 123, 49, 49, 14, 14, 5, 1, 14, 14] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 634
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043056 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043056
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043056/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043056
Building REAL250005043057
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043057'
/scratch/stefan/7916125/working/building/REAL250005043057 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043057

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043057/0 /scratch/stefan/7916125/working/building/REAL250005043057 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/165
`/scratch/stefan/7916125/working/3D/165' -> `0.mol2'
Preparing input files

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

`REAL250005043057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043057 none C[C@@H](O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
576  conformations in input
total number of sets (complete confs): 576
using faster count positions algorithm for large data
unique positions, atoms: [143, 50, 143, 138, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 1, 143, 143, 143, 429, 50, 10, 10, 1, 1, 6, 29, 1, 1] 576
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 984
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043057 none C[C@@H](O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
576  conformations in input
total number of sets (complete confs): 576
using faster count positions algorithm for large data
unique positions, atoms: [192, 166, 192, 191, 166, 166, 93, 29, 29, 29, 29, 8, 29, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 192, 192, 192, 576, 166, 93, 93, 29, 29, 8, 1, 29, 29] 576
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1274
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043057 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043057
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043057/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043057
Building REAL250005043058
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043058'
/scratch/stefan/7916125/working/building/REAL250005043058 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043058

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043058/0 /scratch/stefan/7916125/working/building/REAL250005043058 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/166
`/scratch/stefan/7916125/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043058 none O=C(C=CCO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
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, 35, 35, 99, 99, 165, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 99, 99, 165, 165, 495, 35, 7, 7, 1, 1, 6, 16, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 1126
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043058 none O=C(C=CCO)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
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: [137, 137, 137, 195, 195, 201, 55, 16, 16, 16, 16, 4, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 16, 195, 195, 201, 201, 603, 137, 55, 55, 16, 16, 4, 1, 16, 16] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043058 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043058
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043058/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043058
Building REAL250005043059
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043059'
/scratch/stefan/7916125/working/building/REAL250005043059 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043059

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043059/0 /scratch/stefan/7916125/working/building/REAL250005043059 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/167
`/scratch/stefan/7916125/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005043059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043059 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 42, 57, 57, 57, 42, 8, 8, 1, 1, 6, 23, 1, 1, 57, 57, 57, 57, 57] 86
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 171
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043059 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 23, 23, 23, 23, 8, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 86, 86, 86, 86, 86, 62, 62, 23, 23, 9, 1, 23, 23, 86, 86, 86, 86, 86] 86
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 302
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043059 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 28, 57, 57, 57, 57, 57, 82, 82, 82, 86, 86, 86, 86, 86, 57, 1, 1, 1, 1, 10, 28, 28, 57, 57, 82, 86, 57, 57, 1, 1, 1, 1, 1] 86
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 277
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043059 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043059
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043059/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043059
Building REAL250005043060
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043060'
/scratch/stefan/7916125/working/building/REAL250005043060 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043060

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043060/0 /scratch/stefan/7916125/working/building/REAL250005043060 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/168
`/scratch/stefan/7916125/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043060 none CON=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [115, 97, 97, 45, 45, 45, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 115, 115, 115, 97, 45, 7, 7, 1, 1, 6, 26, 1, 1] 137
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 347
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043060 none CON=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 123, 123, 123, 71, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 137, 137, 137, 137, 123, 71, 71, 26, 26, 8, 1, 26, 26] 137
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 467
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043060 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043060
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043060/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043060
Building REAL250005043061
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043061'
/scratch/stefan/7916125/working/building/REAL250005043061 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043061

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043061/0 /scratch/stefan/7916125/working/building/REAL250005043061 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/169
`/scratch/stefan/7916125/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1)

`REAL250005043061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043061 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 50, 158, 158, 158, 50, 10, 10, 1, 1, 6, 17, 1, 1, 158, 158, 158, 158] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 445
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043061 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [151, 151, 62, 17, 17, 17, 17, 5, 17, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 151, 201, 201, 201, 151, 62, 62, 17, 17, 6, 1, 17, 17, 201, 201, 201, 201] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 651
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043061 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 11, 11, 76, 158, 158, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 158, 1, 1, 1, 1, 11, 76, 76, 158, 158, 201, 201, 158, 158, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 681
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043061 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043061
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043061/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043061
Building REAL250005043062
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043062'
/scratch/stefan/7916125/working/building/REAL250005043062 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043062

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043062/0 /scratch/stefan/7916125/working/building/REAL250005043062 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/170
`/scratch/stefan/7916125/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043062 none CC=C(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [118, 118, 50, 118, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 1, 118, 118, 118, 118, 50, 10, 10, 1, 1, 6, 21, 1, 1] 169
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 361
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043062 none CC=C(F)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 141, 169, 141, 141, 77, 21, 21, 21, 21, 7, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 169, 169, 169, 169, 141, 77, 77, 21, 21, 8, 1, 21, 21] 169
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 574
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043062 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043062
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043062/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043062
Building REAL250005043063
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043063'
/scratch/stefan/7916125/working/building/REAL250005043063 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043063

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043063/0 /scratch/stefan/7916125/working/building/REAL250005043063 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/171
`/scratch/stefan/7916125/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043063 none CC(CO)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [123, 39, 123, 171, 39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 123, 123, 123, 123, 171, 171, 513, 39, 7, 7, 1, 1, 6, 15, 1, 1] 603
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 1234
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043063 none CC(CO)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [196, 130, 196, 201, 130, 130, 55, 15, 15, 15, 15, 3, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 15, 196, 196, 196, 196, 201, 201, 603, 130, 55, 55, 15, 15, 4, 1, 15, 15] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1359
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043063 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043063
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043063/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043063
Building REAL250005043064
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043064'
/scratch/stefan/7916125/working/building/REAL250005043064 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043064

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043064/0 /scratch/stefan/7916125/working/building/REAL250005043064 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/172
`/scratch/stefan/7916125/working/3D/172' -> `0.mol2'
Preparing input files

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

`REAL250005043064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043064 none C[C@H](O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
579  conformations in input
total number of sets (complete confs): 579
using faster count positions algorithm for large data
unique positions, atoms: [142, 49, 142, 142, 49, 49, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 142, 142, 142, 426, 49, 10, 10, 1, 1, 6, 28, 1, 1] 579
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 984
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043064 none C[C@H](O)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
579  conformations in input
total number of sets (complete confs): 579
using faster count positions algorithm for large data
unique positions, atoms: [193, 167, 193, 193, 167, 167, 92, 28, 28, 28, 28, 9, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 193, 193, 193, 579, 167, 92, 92, 28, 28, 9, 1, 28, 28] 579
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1282
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043064 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043064
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043064/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043064
Building REAL250005043065
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043065'
/scratch/stefan/7916125/working/building/REAL250005043065 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043065

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043065/0 /scratch/stefan/7916125/working/building/REAL250005043065 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/173
`/scratch/stefan/7916125/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043065 none C=C1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 78, 156, 156, 156, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 156, 1, 1, 1, 1, 1, 13, 78, 78, 156, 156, 201, 201, 156, 156] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 682
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043065 none C=C1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [156, 156, 156, 44, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 156, 156, 156, 156, 156, 44, 8, 8, 1, 1, 6, 15, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34])
total number of confs: 429
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043065 none C=C1CC1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 135, 135, 135, 58, 15, 15, 15, 15, 5, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 201, 201, 201, 201, 201, 135, 58, 58, 15, 15, 5, 1, 15, 15] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043065 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043065
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043065/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043065
Building REAL250005043066
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043066'
/scratch/stefan/7916125/working/building/REAL250005043066 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043066

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043066/0 /scratch/stefan/7916125/working/building/REAL250005043066 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/174
`/scratch/stefan/7916125/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043066 none CC(CF)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 109, 153, 40, 40, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 109, 109, 109, 109, 153, 153, 40, 7, 7, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35])
total number of confs: 650
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043066 none CC(CF)C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 198, 201, 126, 126, 54, 14, 14, 14, 14, 3, 14, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 198, 198, 198, 198, 201, 201, 126, 54, 54, 14, 14, 3, 1, 14, 14] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 739
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043066 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043066
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043066/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043066
Building REAL250005043067
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043067'
/scratch/stefan/7916125/working/building/REAL250005043067 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043067

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043067/0 /scratch/stefan/7916125/working/building/REAL250005043067 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/175
`/scratch/stefan/7916125/working/3D/175' -> `0.mol2'
Preparing input files

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

`REAL250005043067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043067 none C=C(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 111, 155, 29, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 155, 155, 155, 155, 155, 111, 111, 29, 7, 7, 1, 1, 6, 22, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 565
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043067 none C=C(C)CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 201, 120, 120, 120, 68, 22, 22, 22, 22, 5, 22, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 201, 201, 195, 195, 120, 68, 68, 22, 22, 6, 1, 22, 22] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 781
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043067 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043067
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043067/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043067
Building REAL250005043068
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043068'
/scratch/stefan/7916125/working/building/REAL250005043068 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043068

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043068/0 /scratch/stefan/7916125/working/building/REAL250005043068 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/176
`/scratch/stefan/7916125/working/3D/176' -> `0.mol2'
Preparing input files

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

`REAL250005043068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043068 none CC=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 52, 52, 52, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 28, 1, 120, 120, 120, 120, 120, 52, 10, 10, 1, 1, 6, 28, 1, 1] 159
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043068 none CC=CC(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 140, 140, 140, 85, 28, 28, 28, 28, 9, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 159, 159, 159, 159, 159, 140, 85, 85, 28, 28, 9, 1, 28, 28] 159
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 547
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043068 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043068
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043068/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043068
Building REAL250005043069
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043069'
/scratch/stefan/7916125/working/building/REAL250005043069 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043069

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043069/0 /scratch/stefan/7916125/working/building/REAL250005043069 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/177
`/scratch/stefan/7916125/working/3D/177' -> `0.mol2'
Preparing input files

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

`REAL250005043069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043069 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 146, 146, 146, 146, 146, 200, 200, 200, 201, 201, 201, 201, 201, 146, 2, 2, 2, 1, 1, 12, 69, 69, 146, 146, 200, 201, 146, 146] 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])
total number of confs: 663
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043069 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [146, 146, 146, 146, 50, 146, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 146, 146, 146, 146, 146, 50, 9, 9, 1, 1, 6, 19, 1, 1] 201
rigid atoms, others: [33, 34, 37, 38, 9, 10, 11, 12, 13, 14, 15, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36])
total number of confs: 418
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043069 none C[C@@H]1C[C@H]1C(=O)NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)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.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 130, 201, 130, 130, 62, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 1, 1, 1, 19, 201, 201, 201, 201, 201, 130, 62, 62, 19, 19, 5, 1, 19, 19] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 642
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043069 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043069
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043069/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043069
Building REAL250005043070
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043070'
/scratch/stefan/7916125/working/building/REAL250005043070 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043070

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043070/0 /scratch/stefan/7916125/working/building/REAL250005043070 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/178
`/scratch/stefan/7916125/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1)

`REAL250005043070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043070 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 46, 143, 143, 143, 46, 10, 10, 1, 1, 6, 20, 1, 1, 429, 143, 143, 143, 143] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 18, 26, 27, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 841
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043070 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 76, 20, 20, 20, 20, 6, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 167, 201, 201, 201, 167, 76, 76, 20, 20, 7, 1, 20, 20, 603, 201, 201, 201, 201] 603
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1263
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043070 none O=C(NC[C@H]1C[C@H](NC(=O)C2=CC(=O)[N-]O2)C1)C1(O)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 66, 143, 143, 143, 143, 143, 199, 199, 199, 201, 201, 201, 201, 201, 143, 1, 1, 1, 1, 12, 66, 66, 143, 143, 199, 201, 143, 143, 6, 1, 1, 1, 1] 603
rigid atoms, others: [1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 677
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043070 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043070
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043070/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043070
Building REAL250005043071
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043071'
/scratch/stefan/7916125/working/building/REAL250005043071 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043071

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043071/0 /scratch/stefan/7916125/working/building/REAL250005043071 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/179
`/scratch/stefan/7916125/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043071 none O=C(CC1CC1)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 3, 1, 1, 1, 1, 24, 24, 81, 81, 81, 81, 81, 166, 201, 201, 201, 201, 201, 201, 201, 201, 81, 3, 3, 1, 1, 1, 1, 1, 24, 81, 81, 166, 166, 201, 201, 81, 81] 201
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])
total number of confs: 745
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043071 none O=C(CC1CC1)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 50, 81, 81, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 47, 47, 47, 47, 47, 1, 50, 50, 81, 81, 81, 81, 81, 6, 1, 1, 7, 7, 41, 47, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 397
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043071 none O=C(CC1CC1)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 176, 201, 201, 47, 47, 47, 47, 14, 47, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 176, 176, 201, 201, 201, 201, 201, 110, 47, 47, 14, 14, 4, 1, 47, 47] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 767
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043071 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043071
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043071/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043071
Building REAL250005043072
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043072'
/scratch/stefan/7916125/working/building/REAL250005043072 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043072

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043072/0 /scratch/stefan/7916125/working/building/REAL250005043072 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/180
`/scratch/stefan/7916125/working/3D/180' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043072 none CC(C)(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 80, 80, 80, 80, 80, 1, 47, 47, 47, 47, 47, 47, 6, 1, 1, 9, 9, 49, 80, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043072 none CC(C)(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 147, 201, 201, 147, 147, 80, 80, 80, 80, 27, 80, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 147, 80, 80, 26, 26, 5, 1, 80, 80] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 712
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043072 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043072
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043072/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043072
Building REAL250005043073
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043073'
/scratch/stefan/7916125/working/building/REAL250005043073 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043073

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043073/0 /scratch/stefan/7916125/working/building/REAL250005043073 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/181
`/scratch/stefan/7916125/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043073 none COCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [93, 52, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 58, 58, 58, 58, 58, 1, 93, 93, 93, 52, 52, 6, 1, 1, 7, 7, 42, 58, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043073 none COCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 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: [201, 201, 136, 136, 136, 58, 58, 58, 58, 19, 58, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 136, 58, 58, 19, 19, 4, 1, 58, 58] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 739
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043073 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043073
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043073/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043073
Building REAL250005043074
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043074'
/scratch/stefan/7916125/working/building/REAL250005043074 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043074

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043074/0 /scratch/stefan/7916125/working/building/REAL250005043074 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/182
`/scratch/stefan/7916125/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043074 none CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 46, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 59, 59, 59, 59, 59, 1, 74, 74, 74, 74, 74, 46, 46, 6, 1, 1, 7, 7, 45, 59, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 37, 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, 32, 33, 34, 35])
total number of confs: 540
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043074 none CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 133, 133, 133, 59, 59, 59, 59, 20, 59, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 197, 197, 133, 59, 59, 19, 19, 4, 1, 59, 59] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043074 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043074
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043074/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043074
Building REAL250005043075
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043075'
/scratch/stefan/7916125/working/building/REAL250005043075 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043075

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043075/0 /scratch/stefan/7916125/working/building/REAL250005043075 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/183
`/scratch/stefan/7916125/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043075 none CC(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 28, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 68, 68, 68, 68, 68, 1, 38, 38, 38, 38, 38, 38, 38, 28, 28, 6, 1, 1, 9, 9, 47, 68, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 352
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043075 none CC(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 117, 117, 117, 68, 68, 68, 68, 25, 68, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 68, 68, 25, 25, 4, 1, 68, 68] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 742
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043075 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043075
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043075/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043075
Building REAL250005043076
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043076'
/scratch/stefan/7916125/working/building/REAL250005043076 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043076

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043076/0 /scratch/stefan/7916125/working/building/REAL250005043076 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/184
`/scratch/stefan/7916125/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043076 none CC1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 47, 47, 47, 47, 47, 138, 201, 201, 201, 201, 201, 201, 201, 201, 47, 2, 2, 2, 1, 1, 1, 1, 12, 47, 47, 138, 138, 201, 201, 47, 47] 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])
total number of confs: 724
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043076 none CC1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 80, 80, 80, 80, 80, 1, 47, 47, 47, 47, 47, 47, 47, 6, 1, 1, 9, 9, 49, 80, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043076 none CC1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 139, 139, 139, 80, 80, 80, 80, 27, 80, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 139, 80, 80, 27, 27, 5, 1, 80, 80] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043076 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043076
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043076/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043076
Building REAL250005043077
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043077'
/scratch/stefan/7916125/working/building/REAL250005043077 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043077

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043077/0 /scratch/stefan/7916125/working/building/REAL250005043077 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/185
`/scratch/stefan/7916125/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043077 none CCOCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [78, 74, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40, 61, 61, 61, 61, 61, 1, 78, 78, 78, 78, 78, 33, 33, 6, 1, 1, 7, 7, 40, 61, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043077 none CCOCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 131, 131, 131, 61, 61, 61, 61, 23, 61, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 200, 200, 131, 61, 61, 22, 22, 4, 1, 61, 61] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 758
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043077 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043077
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043077/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043077
Building REAL250005043078
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043078'
/scratch/stefan/7916125/working/building/REAL250005043078 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043078

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043078/0 /scratch/stefan/7916125/working/building/REAL250005043078 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/186
`/scratch/stefan/7916125/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043078 none CC(C)=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 96, 96, 96, 96, 96, 1, 28, 28, 28, 28, 28, 28, 28, 6, 1, 1, 10, 10, 54, 96, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 272
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043078 none CC(C)=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 160, 160, 160, 96, 96, 96, 96, 36, 96, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 160, 96, 96, 36, 36, 7, 1, 96, 96] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 666
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043078 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043078
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043078/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043078
Building REAL250005043079
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043079'
/scratch/stefan/7916125/working/building/REAL250005043079 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043079

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043079/0 /scratch/stefan/7916125/working/building/REAL250005043079 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/187
`/scratch/stefan/7916125/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043079 none CSCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [101, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 36, 36, 36, 36, 36, 36, 1, 94, 101, 101, 45, 45, 6, 1, 1, 7, 7, 36, 36, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043079 none CSCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 186, 100, 100, 100, 36, 36, 36, 36, 10, 36, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 186, 186, 100, 36, 36, 10, 10, 2, 1, 36, 36] 201
rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043079 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043079
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043079/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043079
Building REAL250005043080
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043080'
/scratch/stefan/7916125/working/building/REAL250005043080 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043080

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043080/0 /scratch/stefan/7916125/working/building/REAL250005043080 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/188
`/scratch/stefan/7916125/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043080 none CCCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 55, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 37, 37, 37, 40, 40, 40, 40, 40, 1, 70, 70, 70, 70, 70, 69, 69, 45, 45, 6, 1, 1, 6, 6, 37, 40, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 467
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043080 none CCCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 105, 105, 105, 40, 40, 40, 40, 13, 40, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 195, 195, 105, 40, 40, 12, 12, 4, 1, 40, 40] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 767
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043080 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043080
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043080/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043080
Building REAL250005043081
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043081'
/scratch/stefan/7916125/working/building/REAL250005043081 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043081

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043081/0 /scratch/stefan/7916125/working/building/REAL250005043081 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/189
`/scratch/stefan/7916125/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043081 none CC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 6, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 53, 53, 53, 109, 109, 109, 109, 109, 1, 41, 41, 41, 41, 41, 41, 41, 6, 1, 1, 9, 9, 53, 109, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 21, 37, 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, 32, 33, 34, 35])
total number of confs: 352
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043081 none CC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 109, 109, 109, 109, 39, 109, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 173, 109, 109, 39, 39, 6, 1, 109, 109] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 706
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043081 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043081
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043081/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043081
Building REAL250005043082
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043082'
/scratch/stefan/7916125/working/building/REAL250005043082 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043082

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043082/0 /scratch/stefan/7916125/working/building/REAL250005043082 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/190
`/scratch/stefan/7916125/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043082 none CCC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 55, 55, 55, 55, 55, 1, 50, 50, 50, 50, 50, 32, 32, 32, 32, 6, 1, 1, 7, 7, 41, 55, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043082 none CCC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 120, 200, 120, 120, 55, 55, 55, 55, 18, 55, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 200, 200, 200, 200, 120, 55, 55, 18, 18, 4, 1, 55, 55] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 743
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043082 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043082
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043082/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043082
Building REAL250005043083
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043083'
/scratch/stefan/7916125/working/building/REAL250005043083 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043083

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043083/0 /scratch/stefan/7916125/working/building/REAL250005043083 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/191
`/scratch/stefan/7916125/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043083 none COC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 51, 6, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 63, 63, 63, 63, 63, 1, 72, 72, 72, 51, 51, 51, 51, 6, 1, 1, 7, 7, 41, 63, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043083 none COC(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 134, 201, 134, 134, 63, 63, 63, 63, 22, 63, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 134, 63, 63, 21, 21, 3, 1, 63, 63] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 742
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043083 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043083
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043083/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043083
Building REAL250005043084
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043084'
/scratch/stefan/7916125/working/building/REAL250005043084 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043084

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043084/0 /scratch/stefan/7916125/working/building/REAL250005043084 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/192
`/scratch/stefan/7916125/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043084 none C=CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 44, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 32, 32, 32, 75, 75, 75, 75, 75, 1, 88, 88, 88, 44, 44, 43, 43, 6, 1, 1, 5, 5, 32, 75, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 442
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043084 none C=CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 126, 126, 126, 75, 75, 75, 75, 33, 75, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 201, 201, 126, 75, 75, 32, 32, 5, 1, 75, 75] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 791
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043084 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043084
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043084/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043084
Building REAL250005043085
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043085'
/scratch/stefan/7916125/working/building/REAL250005043085 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043085

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043085/0 /scratch/stefan/7916125/working/building/REAL250005043085 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/193
`/scratch/stefan/7916125/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043085 none CC(C#N)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 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: [52, 6, 52, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 66, 66, 66, 66, 66, 1, 52, 52, 52, 52, 6, 1, 1, 9, 9, 48, 66, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 319
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043085 none CC(C#N)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 134, 201, 201, 134, 134, 66, 66, 66, 66, 19, 66, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 134, 66, 66, 19, 19, 4, 1, 66, 66] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 735
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043085 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043085
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043085/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043085
Building REAL250005043086
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043086'
/scratch/stefan/7916125/working/building/REAL250005043086 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043086

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043086/0 /scratch/stefan/7916125/working/building/REAL250005043086 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/194
`/scratch/stefan/7916125/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043086 none CC=C(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 81, 81, 81, 81, 81, 1, 43, 43, 43, 43, 43, 43, 43, 6, 1, 1, 9, 9, 51, 81, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 278
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043086 none CC=C(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 201, 149, 149, 81, 81, 81, 81, 30, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 149, 81, 81, 29, 29, 5, 1, 81, 81] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 677
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043086 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043086
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043086/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043086
Building REAL250005043087
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043087'
/scratch/stefan/7916125/working/building/REAL250005043087 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043087

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043087/0 /scratch/stefan/7916125/working/building/REAL250005043087 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/195
`/scratch/stefan/7916125/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043087 none CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [49, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 57, 118, 118, 118, 118, 118, 1, 49, 49, 49, 49, 49, 6, 1, 1, 10, 10, 57, 118, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 20, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 399
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043087 none CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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: [201, 168, 168, 168, 118, 118, 118, 118, 42, 118, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 168, 118, 118, 42, 42, 8, 1, 118, 118] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 735
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043087 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043087
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043087/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043087
Building REAL250005043088
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043088'
/scratch/stefan/7916125/working/building/REAL250005043088 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043088

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043088/0 /scratch/stefan/7916125/working/building/REAL250005043088 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/196
`/scratch/stefan/7916125/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043088 none COCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 53, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 34, 34, 34, 59, 59, 59, 59, 59, 1, 77, 77, 77, 53, 53, 39, 39, 6, 1, 1, 6, 6, 34, 59, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 383
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043088 none COCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 118, 118, 118, 59, 59, 59, 59, 23, 59, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 191, 191, 118, 59, 59, 23, 23, 3, 1, 59, 59] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043088 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043088
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043088/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043088
Building REAL250005043089
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043089'
/scratch/stefan/7916125/working/building/REAL250005043089 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043089

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043089/0 /scratch/stefan/7916125/working/building/REAL250005043089 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/197
`/scratch/stefan/7916125/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043089 none CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39, 66, 66, 66, 66, 66, 1, 6, 6, 6, 6, 1, 1, 9, 9, 39, 66, 1, 1] 69
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 19, 24, 25, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 26, 27, 28, 29])
total number of confs: 161
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043089 none CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 66, 66, 66, 66, 35, 66, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 66, 69, 69, 69, 69, 66, 66, 35, 35, 10, 1, 66, 66] 69
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 236
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043089 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043089
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043089/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043089
Building REAL250005043090
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043090'
/scratch/stefan/7916125/working/building/REAL250005043090 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043090

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043090/0 /scratch/stefan/7916125/working/building/REAL250005043090 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/198
`/scratch/stefan/7916125/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043090 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 42, 42, 1, 53, 92, 92, 92, 92, 92, 53, 8, 8, 1, 1, 6, 42, 42, 42, 42, 42, 1, 1, 92] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 15, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 288
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043090 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 127, 42, 42, 42, 42, 11, 42, 11, 1, 11, 1, 1, 1, 42, 197, 201, 201, 201, 201, 201, 197, 127, 127, 42, 42, 11, 1, 1, 1, 1, 1, 42, 42, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 693
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043090 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 34, 92, 92, 92, 92, 92, 149, 149, 149, 201, 201, 92, 1, 1, 1, 1, 1, 1, 7, 34, 34, 92, 92, 149, 201, 201, 201, 201, 201, 92, 92, 1] 201
rigid atoms, others: [1, 35, 16, 17, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 651
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043090 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043090
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043090/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043090
Building REAL250005043091
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043091'
/scratch/stefan/7916125/working/building/REAL250005043091 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043091

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043091/0 /scratch/stefan/7916125/working/building/REAL250005043091 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/199
`/scratch/stefan/7916125/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043091 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 41, 41, 1, 46, 89, 89, 89, 89, 89, 46, 8, 8, 1, 1, 6, 41, 41, 41, 41, 41, 41, 41, 1, 1, 89] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 16, 36, 26, 27, 37] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043091 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 120, 41, 41, 41, 41, 11, 41, 11, 1, 11, 1, 1, 1, 1, 41, 198, 201, 201, 201, 201, 201, 198, 120, 120, 41, 41, 11, 1, 1, 1, 1, 1, 1, 1, 41, 41, 201] 201
rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043091 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 89, 89, 89, 89, 89, 144, 144, 144, 201, 201, 201, 89, 1, 1, 1, 1, 1, 1, 7, 32, 32, 89, 89, 144, 201, 201, 201, 201, 201, 201, 201, 89, 89, 1] 201
rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 636
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043091 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043091
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043091/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043091
Building REAL250005043092
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043092'
/scratch/stefan/7916125/working/building/REAL250005043092 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043092

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043092/0 /scratch/stefan/7916125/working/building/REAL250005043092 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/200
`/scratch/stefan/7916125/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043092 none NC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 72, 72, 72, 72, 72, 1, 36, 36, 6, 1, 1, 9, 9, 49, 72, 1, 1] 132
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 21, 25, 26, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043092 none NC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [132, 123, 132, 123, 123, 72, 72, 72, 72, 22, 72, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 72, 132, 132, 123, 72, 72, 22, 22, 5, 1, 72, 72] 132
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 409
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043092 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043092
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043092/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043092
Building REAL250005043093
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043093'
/scratch/stefan/7916125/working/building/REAL250005043093 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043093

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043093/0 /scratch/stefan/7916125/working/building/REAL250005043093 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/201
`/scratch/stefan/7916125/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043093 none CC(C)(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 48, 48, 48, 74, 74, 74, 74, 74, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 10, 10, 48, 74, 1, 1] 103
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39] 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, 35, 36, 37, 38])
total number of confs: 220
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043093 none CC(C)(C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 99, 103, 103, 99, 99, 74, 74, 74, 74, 32, 74, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 74, 103, 103, 103, 103, 103, 103, 103, 103, 103, 99, 74, 74, 31, 31, 8, 1, 74, 74] 103
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 354
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043093 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043093
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043093/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043093
Building REAL250005043094
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043094'
/scratch/stefan/7916125/working/building/REAL250005043094 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043094

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043094/0 /scratch/stefan/7916125/working/building/REAL250005043094 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/202
`/scratch/stefan/7916125/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N[C@H]2C[C@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005043094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043094 none CC1(C(=O)N[C@H]2C[C@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 7, 7, 29, 29, 29, 29, 29, 123, 201, 201, 201, 201, 201, 201, 201, 201, 29, 1, 1, 2, 2, 2, 7, 29, 29, 123, 123, 201, 201, 29, 29, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043094 none CC1(C(=O)N[C@H]2C[C@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 78, 78, 78, 78, 78, 1, 29, 29, 29, 29, 29, 6, 1, 1, 9, 9, 46, 78, 1, 1, 29, 29, 29, 29] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 20, 27, 28] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 240
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043094 none CC1(C(=O)N[C@H]2C[C@H](CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 121, 121, 121, 78, 78, 78, 78, 27, 78, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 121, 78, 78, 27, 27, 6, 1, 78, 78, 201, 201, 201, 201] 201
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 635
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043094 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043094
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043094/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043094
Building REAL250005043095
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043095'
/scratch/stefan/7916125/working/building/REAL250005043095 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043095

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043095/0 /scratch/stefan/7916125/working/building/REAL250005043095 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/203
`/scratch/stefan/7916125/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043095 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 47, 47, 140, 201, 201, 201, 201, 201, 201, 201, 201, 47, 2, 2, 2, 1, 1, 13, 47, 47, 140, 140, 201, 201, 47, 47] 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])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043095 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [47, 47, 47, 47, 6, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 81, 81, 81, 81, 81, 1, 47, 47, 47, 47, 47, 6, 1, 1, 9, 9, 50, 81, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043095 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 144, 201, 144, 144, 81, 81, 81, 81, 27, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 144, 81, 81, 26, 26, 6, 1, 81, 81] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043095 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043095
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043095/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043095
Building REAL250005043096
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043096'
/scratch/stefan/7916125/working/building/REAL250005043096 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043096

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043096/0 /scratch/stefan/7916125/working/building/REAL250005043096 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/204
`/scratch/stefan/7916125/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043096 none CCC(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [57, 42, 6, 42, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 58, 58, 58, 58, 58, 1, 68, 68, 68, 68, 68, 42, 6, 1, 1, 7, 7, 45, 58, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 481
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043096 none CCC(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 131, 195, 131, 131, 58, 58, 58, 58, 20, 58, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 195, 131, 58, 58, 20, 20, 4, 1, 58, 58] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 739
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043096 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043096
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043096/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043096
Building REAL250005043097
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043097'
/scratch/stefan/7916125/working/building/REAL250005043097 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043097

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043097/0 /scratch/stefan/7916125/working/building/REAL250005043097 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/205
`/scratch/stefan/7916125/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043097 none O=C(CCCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 42, 54, 93, 1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 27, 27, 27, 27, 27, 1, 42, 42, 68, 68, 87, 87, 6, 1, 1, 6, 6, 27, 27, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 533
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043097 none O=C(CCCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 70, 70, 186, 194, 201, 27, 27, 27, 27, 8, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 186, 186, 201, 201, 201, 201, 70, 27, 27, 8, 8, 1, 1, 27, 27] 201
rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37])
total number of confs: 817
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043097 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043097
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043097/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043097
Building REAL250005043098
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043098'
/scratch/stefan/7916125/working/building/REAL250005043098 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043098

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043098/0 /scratch/stefan/7916125/working/building/REAL250005043098 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/206
`/scratch/stefan/7916125/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043098 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 50, 137, 201, 201, 201, 201, 201, 201, 201, 201, 50, 2, 2, 2, 1, 1, 13, 50, 50, 137, 137, 201, 201, 50, 50] 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])
total number of confs: 718
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043098 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [50, 50, 50, 50, 6, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 48, 79, 79, 79, 79, 79, 1, 50, 50, 50, 50, 50, 6, 1, 1, 9, 9, 48, 79, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
total number of confs: 288
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043098 none C[C@H]1C[C@@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 138, 201, 138, 138, 79, 79, 79, 79, 27, 79, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 138, 79, 79, 26, 26, 6, 1, 79, 79] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043098 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043098
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043098/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043098
Building REAL250005043099
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043099'
/scratch/stefan/7916125/working/building/REAL250005043099 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043099

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043099/0 /scratch/stefan/7916125/working/building/REAL250005043099 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/207
`/scratch/stefan/7916125/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043099 none O=C(CO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
354  conformations in input
total number of sets (complete confs): 354
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 49, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 68, 68, 68, 68, 68, 1, 49, 49, 147, 6, 1, 1, 9, 9, 47, 68, 1, 1] 354
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 461
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043099 none O=C(CO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
354  conformations in input
total number of sets (complete confs): 354
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 118, 68, 68, 68, 68, 23, 68, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 68, 118, 118, 354, 114, 68, 68, 22, 22, 5, 1, 68, 68] 354
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043099 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043099
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043099/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043099
Building REAL250005043100
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043100'
/scratch/stefan/7916125/working/building/REAL250005043100 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043100

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043100/0 /scratch/stefan/7916125/working/building/REAL250005043100 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/208
`/scratch/stefan/7916125/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1)

`REAL250005043100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043100 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 41, 41, 1, 50, 79, 79, 79, 79, 79, 50, 8, 8, 1, 1, 6, 41, 41, 41, 41, 41, 1, 1, 79] 155
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 265
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043100 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 109, 41, 41, 41, 41, 11, 41, 11, 1, 11, 1, 1, 1, 1, 41, 153, 155, 155, 155, 155, 155, 153, 109, 109, 41, 41, 11, 1, 1, 1, 1, 1, 41, 41, 155] 155
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 565
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043100 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 7, 29, 79, 79, 79, 79, 79, 126, 126, 126, 155, 155, 155, 79, 1, 1, 1, 1, 1, 1, 7, 29, 29, 79, 79, 126, 155, 155, 155, 155, 155, 79, 79, 1] 155
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 502
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043100 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043100
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043100/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043100
Building REAL250005043101
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043101'
/scratch/stefan/7916125/working/building/REAL250005043101 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043101

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043101/0 /scratch/stefan/7916125/working/building/REAL250005043101 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/209
`/scratch/stefan/7916125/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043101 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 47, 47, 47, 1, 48, 90, 90, 90, 90, 90, 48, 8, 8, 1, 1, 6, 47, 47, 47, 47, 47, 1, 1, 90] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 298
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043101 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 47, 47, 47, 47, 11, 47, 11, 1, 11, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 125, 125, 47, 47, 11, 1, 1, 1, 1, 1, 47, 47, 201] 201
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 709
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043101 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 28, 90, 90, 90, 90, 90, 158, 158, 158, 201, 201, 201, 90, 1, 1, 1, 1, 1, 1, 5, 28, 28, 90, 90, 158, 201, 201, 201, 201, 201, 90, 90, 1] 201
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 639
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043101 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043101
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043101/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043101
Building REAL250005043102
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043102'
/scratch/stefan/7916125/working/building/REAL250005043102 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043102

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043102/0 /scratch/stefan/7916125/working/building/REAL250005043102 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/210
`/scratch/stefan/7916125/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043102 none O=C(C=CCO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 27, 27, 73, 1, 1, 1, 1, 1, 1, 1, 6, 37, 37, 37, 84, 84, 84, 84, 84, 1, 27, 27, 73, 73, 219, 6, 1, 1, 6, 6, 37, 84, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043102 none O=C(C=CCO)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 1, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 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]
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: [156, 156, 156, 201, 201, 201, 84, 84, 84, 84, 35, 84, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 603, 156, 84, 84, 35, 35, 7, 1, 84, 84] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043102 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043102
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043102/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043102
Building REAL250005043103
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043103'
/scratch/stefan/7916125/working/building/REAL250005043103 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043103

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043103/0 /scratch/stefan/7916125/working/building/REAL250005043103 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/211
`/scratch/stefan/7916125/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043103 none CCC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 35, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 40, 58, 58, 58, 58, 58, 1, 67, 67, 67, 67, 67, 35, 35, 6, 1, 1, 7, 7, 40, 58, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 389
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043103 none CCC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 122, 122, 122, 58, 58, 58, 58, 23, 58, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 164, 164, 122, 58, 58, 23, 23, 4, 1, 58, 58] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 757
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043103 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043103
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043103/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043103
Building REAL250005043104
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043104'
/scratch/stefan/7916125/working/building/REAL250005043104 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043104

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043104/0 /scratch/stefan/7916125/working/building/REAL250005043104 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/212
`/scratch/stefan/7916125/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043104 none C#CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [67, 67, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 39, 44, 44, 44, 44, 44, 1, 67, 67, 67, 43, 43, 6, 1, 1, 7, 7, 39, 44, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043104 none C#CCCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 181, 107, 107, 107, 44, 44, 44, 44, 14, 44, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 181, 181, 107, 44, 44, 14, 14, 3, 1, 44, 44] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 766
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043104 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043104
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043104/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043104
Building REAL250005043105
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043105'
/scratch/stefan/7916125/working/building/REAL250005043105 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043105

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043105/0 /scratch/stefan/7916125/working/building/REAL250005043105 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/213
`/scratch/stefan/7916125/working/3D/213' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043105 none C=CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [96, 49, 6, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 52, 52, 52, 52, 52, 1, 96, 96, 96, 49, 147, 6, 1, 1, 7, 7, 42, 52, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 571
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043105 none C=CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 134, 201, 134, 134, 52, 52, 52, 52, 16, 52, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 603, 134, 52, 52, 16, 16, 4, 1, 52, 52] 603
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043105 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043105
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043105/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043105
Building REAL250005043106
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043106'
/scratch/stefan/7916125/working/building/REAL250005043106 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043106

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043106/0 /scratch/stefan/7916125/working/building/REAL250005043106 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/214
`/scratch/stefan/7916125/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043106 none CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [52, 6, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 83, 83, 83, 83, 83, 1, 52, 52, 52, 52, 156, 6, 1, 1, 9, 9, 49, 83, 1, 1] 549
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043106 none CC(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [183, 151, 183, 151, 151, 83, 83, 83, 83, 31, 83, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 183, 183, 183, 183, 549, 151, 83, 83, 31, 31, 7, 1, 83, 83] 549
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043106 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043106
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043106/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043106
Building REAL250005043107
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043107'
/scratch/stefan/7916125/working/building/REAL250005043107 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043107

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043107/0 /scratch/stefan/7916125/working/building/REAL250005043107 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/215
`/scratch/stefan/7916125/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043107 none CC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 75, 75, 75, 75, 75, 1, 35, 35, 35, 6, 1, 1, 9, 9, 49, 75, 1, 1] 153
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 252
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043107 none CC(=O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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]
0  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [153, 131, 153, 131, 131, 75, 75, 75, 75, 26, 75, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 75, 153, 153, 153, 131, 75, 75, 26, 26, 5, 1, 75, 75] 153
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 489
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043107 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043107
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043107/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043107
Building REAL250005043108
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043108'
/scratch/stefan/7916125/working/building/REAL250005043108 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043108

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043108/0 /scratch/stefan/7916125/working/building/REAL250005043108 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/216
`/scratch/stefan/7916125/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043108 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 51, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 48, 48, 48, 1, 51, 86, 86, 86, 86, 86, 51, 10, 10, 1, 1, 6, 48, 48, 48, 48, 1, 1, 86] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 16, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35])
total number of confs: 296
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043108 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 134, 48, 48, 48, 48, 12, 48, 12, 1, 12, 1, 1, 1, 1, 48, 201, 201, 201, 201, 201, 201, 201, 134, 134, 48, 48, 12, 1, 1, 1, 1, 48, 48, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 734
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043108 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [6, 1, 6, 6, 30, 86, 86, 86, 86, 86, 155, 155, 155, 201, 201, 201, 86, 1, 1, 1, 1, 1, 1, 6, 30, 30, 86, 86, 155, 201, 201, 201, 201, 86, 86, 1] 201
rigid atoms, others: [1, 35, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 630
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043108 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043108
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043108/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043108
Building REAL250005043109
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043109'
/scratch/stefan/7916125/working/building/REAL250005043109 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043109

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043109/0 /scratch/stefan/7916125/working/building/REAL250005043109 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/217
`/scratch/stefan/7916125/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043109 none CC=C(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 6, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 93, 93, 93, 93, 93, 1, 48, 48, 48, 48, 6, 1, 1, 10, 10, 52, 93, 1, 1] 188
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 307
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043109 none CC=C(F)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 188, 159, 188, 159, 159, 93, 93, 93, 93, 35, 93, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 93, 188, 188, 188, 188, 159, 93, 93, 35, 35, 8, 1, 93, 93] 188
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 598
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043109 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043109
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043109/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043109
Building REAL250005043110
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043110'
/scratch/stefan/7916125/working/building/REAL250005043110 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043110

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043110/0 /scratch/stefan/7916125/working/building/REAL250005043110 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/218
`/scratch/stefan/7916125/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043110 none CC(CO)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 74, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 50, 50, 50, 50, 50, 1, 36, 36, 36, 36, 74, 74, 222, 6, 1, 1, 7, 7, 41, 50, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 639
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043110 none CC(CO)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [193, 114, 193, 201, 114, 114, 50, 50, 50, 50, 13, 50, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 193, 193, 193, 193, 201, 201, 603, 114, 50, 50, 13, 13, 2, 1, 50, 50] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1363
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043110 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043110
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043110/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043110
Building REAL250005043111
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043111'
/scratch/stefan/7916125/working/building/REAL250005043111 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043111

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043111/0 /scratch/stefan/7916125/working/building/REAL250005043111 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/219
`/scratch/stefan/7916125/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043111 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 47, 47, 47, 1, 53, 88, 88, 88, 88, 88, 53, 10, 10, 1, 1, 6, 141, 47, 47, 47, 47, 1, 1, 88] 603
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 16, 35, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 439
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043111 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 141, 47, 47, 47, 47, 11, 47, 11, 1, 11, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 141, 141, 47, 47, 11, 6, 1, 1, 1, 1, 47, 47, 201] 603
rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 732
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: REAL250005043111 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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, 5, 32, 88, 88, 88, 88, 88, 162, 162, 162, 201, 201, 201, 88, 1, 1, 1, 1, 1, 1, 5, 31, 31, 88, 88, 162, 603, 201, 201, 201, 201, 88, 88, 1] 603
rigid atoms, others: [1, 36, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 1238
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043111 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043111
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043111/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043111
Building REAL250005043112
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043112'
/scratch/stefan/7916125/working/building/REAL250005043112 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043112

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043112/0 /scratch/stefan/7916125/working/building/REAL250005043112 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/220
`/scratch/stefan/7916125/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005043112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043112 none O=C(N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 47, 47, 47, 71, 71, 71, 71, 71, 1, 6, 21, 21, 21, 6, 1, 1, 10, 10, 47, 71, 1, 1, 21, 21, 21, 21, 21] 90
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 18, 24, 25, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 194
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043112 none O=C(N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 71, 71, 71, 71, 31, 71, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 90, 90, 90, 90, 90, 71, 71, 30, 30, 8, 1, 71, 71, 90, 90, 90, 90, 90] 90
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 295
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: REAL250005043112 none O=C(N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 21, 21, 21, 21, 21, 55, 81, 81, 81, 90, 90, 90, 90, 90, 21, 1, 1, 1, 1, 10, 21, 21, 55, 55, 81, 90, 21, 21, 1, 1, 1, 1, 1] 90
rigid atoms, others: [32, 1, 34, 35, 36, 33, 19, 20, 21, 22] set([0, 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])
total number of confs: 300
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043112 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043112
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043112/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043112
Building REAL250005043113
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043113'
/scratch/stefan/7916125/working/building/REAL250005043113 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043113

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043113/0 /scratch/stefan/7916125/working/building/REAL250005043113 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/221
`/scratch/stefan/7916125/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043113 none CC(CF)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 38, 89, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 43, 43, 43, 43, 43, 1, 38, 38, 38, 38, 89, 89, 6, 1, 1, 7, 7, 37, 43, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 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, 32, 33, 34, 35])
total number of confs: 463
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043113 none CC(CF)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 109, 198, 201, 109, 109, 43, 43, 43, 43, 13, 43, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 198, 198, 198, 198, 201, 201, 109, 43, 43, 12, 12, 3, 1, 43, 43] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043113 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043113
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043113/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043113
Building REAL250005043114
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043114'
/scratch/stefan/7916125/working/building/REAL250005043114 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043114

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043114/0 /scratch/stefan/7916125/working/building/REAL250005043114 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/222
`/scratch/stefan/7916125/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043114 none CC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 108, 108, 108, 108, 108, 1, 39, 39, 39, 39, 39, 6, 1, 1, 10, 10, 54, 108, 1, 1] 167
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 311
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043114 none CC=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 139, 139, 139, 108, 108, 108, 108, 40, 108, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 108, 167, 167, 167, 167, 167, 139, 108, 108, 40, 40, 7, 1, 108, 108] 167
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 560
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043114 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043114
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043114/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043114
Building REAL250005043115
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043115'
/scratch/stefan/7916125/working/building/REAL250005043115 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043115

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043115/0 /scratch/stefan/7916125/working/building/REAL250005043115 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/223
`/scratch/stefan/7916125/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043115 none O=C(C=CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens need 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, 39, 39, 108, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 42, 49, 49, 49, 49, 49, 1, 39, 39, 108, 108, 6, 1, 1, 7, 7, 42, 49, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 493
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043115 none O=C(C=CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 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]
0  hydrogens 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, 197, 197, 201, 49, 49, 49, 49, 16, 49, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 197, 197, 201, 201, 125, 49, 49, 16, 16, 4, 1, 49, 49] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 636
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043115 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043115
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043115/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043115
Building REAL250005043116
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043116'
/scratch/stefan/7916125/working/building/REAL250005043116 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005043116 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005043116' -> `/scratch/stefan/7916125/failed/REAL250005043116'
Building REAL250005043117
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043117'
/scratch/stefan/7916125/working/building/REAL250005043117 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043117

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043117/0 /scratch/stefan/7916125/working/building/REAL250005043117 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/224
`/scratch/stefan/7916125/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043117 none C[C@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [52, 6, 52, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 83, 83, 83, 83, 83, 1, 52, 52, 52, 156, 6, 1, 1, 9, 9, 49, 83, 1, 1] 549
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 502
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043117 none C[C@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [183, 150, 183, 183, 150, 150, 83, 83, 83, 83, 32, 83, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 83, 183, 183, 183, 549, 150, 83, 83, 32, 32, 7, 1, 83, 83] 549
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1211
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043117 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043117
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043117/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043117
Building REAL250005043118
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043118'
/scratch/stefan/7916125/working/building/REAL250005043118 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043118

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043118/0 /scratch/stefan/7916125/working/building/REAL250005043118 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/225
`/scratch/stefan/7916125/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043118 none CON=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [48, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 98, 98, 98, 98, 98, 1, 48, 48, 48, 27, 6, 1, 1, 9, 9, 50, 98, 1, 1] 152
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 303
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043118 none CON=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [152, 152, 152, 143, 143, 143, 98, 98, 98, 98, 40, 98, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 98, 152, 152, 152, 152, 143, 98, 98, 40, 40, 8, 1, 98, 98] 152
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 489
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043118 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043118
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043118/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043118
Building REAL250005043119
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043119'
/scratch/stefan/7916125/working/building/REAL250005043119 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043119

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043119/0 /scratch/stefan/7916125/working/building/REAL250005043119 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/226
`/scratch/stefan/7916125/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043119 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 47, 47, 47, 47, 140, 201, 201, 201, 201, 201, 201, 201, 201, 47, 2, 2, 2, 1, 1, 13, 47, 47, 140, 140, 201, 201, 47, 47] 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])
total number of confs: 721
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043119 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [47, 47, 47, 47, 6, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 81, 81, 81, 81, 81, 1, 47, 47, 47, 47, 47, 6, 1, 1, 9, 9, 50, 81, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 13, 14, 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, 33, 34, 35, 36])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043119 none C[C@@H]1C[C@H]1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)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', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 201, 144, 201, 144, 144, 81, 81, 81, 81, 27, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 144, 81, 81, 26, 26, 6, 1, 81, 81] 201
rigid atoms, others: [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, 34, 35, 37, 38])
total number of confs: 634
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043119 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043119
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043119/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043119
Building REAL250005043120
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043120'
/scratch/stefan/7916125/working/building/REAL250005043120 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043120

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043120/0 /scratch/stefan/7916125/working/building/REAL250005043120 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/227
`/scratch/stefan/7916125/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043120 none CC(C)(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [44, 6, 44, 44, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 83, 83, 83, 83, 83, 1, 44, 44, 44, 44, 44, 44, 132, 6, 1, 1, 9, 9, 51, 83, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 458
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043120 none CC(C)(O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 145, 201, 201, 145, 145, 83, 83, 83, 83, 30, 83, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 603, 145, 83, 83, 30, 30, 7, 1, 83, 83] 603
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1334
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043120 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043120
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043120/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043120
Building REAL250005043121
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043121'
/scratch/stefan/7916125/working/building/REAL250005043121 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043121

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043121/0 /scratch/stefan/7916125/working/building/REAL250005043121 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/228
`/scratch/stefan/7916125/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043121 none C=C(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 46, 84, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 38, 47, 47, 47, 47, 47, 1, 84, 84, 84, 84, 84, 46, 46, 6, 1, 1, 7, 7, 38, 47, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 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, 33, 34, 35, 36])
total number of confs: 393
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043121 none C=C(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 113, 113, 113, 47, 47, 47, 47, 19, 47, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 113, 47, 47, 18, 18, 4, 1, 47, 47] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 751
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043121 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043121
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043121/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043121
Building REAL250005043122
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043122'
/scratch/stefan/7916125/working/building/REAL250005043122 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043122

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043122/0 /scratch/stefan/7916125/working/building/REAL250005043122 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/229
`/scratch/stefan/7916125/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043122 none C=CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [109, 55, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 38, 54, 54, 54, 54, 54, 1, 109, 109, 109, 55, 55, 6, 1, 1, 7, 7, 38, 54, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 21, 28, 29] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 465
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043122 none C=CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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: [201, 201, 125, 125, 125, 54, 54, 54, 54, 19, 54, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 125, 54, 54, 19, 19, 3, 1, 54, 54] 201
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 757
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043122 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043122
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043122/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043122
Building REAL250005043123
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043123'
/scratch/stefan/7916125/working/building/REAL250005043123 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043123

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043123/0 /scratch/stefan/7916125/working/building/REAL250005043123 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/230
`/scratch/stefan/7916125/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043123 none C[NH+](C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [38, 36, 38, 38, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 39, 68, 68, 68, 68, 68, 1, 38, 38, 38, 38, 38, 38, 36, 36, 6, 1, 1, 7, 7, 39, 68, 1, 1] 146
rigid atoms, others: [33, 34, 7, 8, 9, 10, 11, 12, 13, 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, 35, 36, 37, 38])
total number of confs: 273
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043123 none C[NH+](C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 123, 123, 123, 68, 68, 68, 68, 28, 68, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 146, 146, 146, 146, 146, 146, 146, 146, 123, 68, 68, 27, 27, 7, 1, 68, 68] 146
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 525
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043123 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043123/1 /scratch/stefan/7916125/working/building/REAL250005043123 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/231
`/scratch/stefan/7916125/working/3D/231' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043123.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043123/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043123 none CN(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [68, 40, 68, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 45, 57, 57, 57, 57, 57, 1, 68, 68, 68, 68, 68, 68, 40, 40, 6, 1, 1, 7, 7, 45, 57, 1, 1] 201
rigid atoms, others: [32, 33, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39] 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, 34, 35, 36, 37])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043123 none CN(C)CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 201, 121, 121, 121, 57, 57, 57, 57, 17, 57, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 198, 198, 121, 57, 57, 17, 17, 3, 1, 57, 57] 201
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043123 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043123
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043123/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043123/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043123
Building REAL250005043124
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043124'
/scratch/stefan/7916125/working/building/REAL250005043124 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043124

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043124/0 /scratch/stefan/7916125/working/building/REAL250005043124 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/232
`/scratch/stefan/7916125/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043124 none N#CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 49, 49, 49, 80, 80, 80, 80, 80, 1, 56, 56, 6, 1, 1, 9, 9, 49, 80, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 21, 25, 26, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043124 none N#CCC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 153, 153, 153, 80, 80, 80, 80, 27, 80, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 80, 201, 201, 153, 80, 80, 26, 26, 5, 1, 80, 80] 201
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043124 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043124
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043124/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043124
Building REAL250005043125
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043125'
/scratch/stefan/7916125/working/building/REAL250005043125 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043125

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043125/0 /scratch/stefan/7916125/working/building/REAL250005043125 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/233
`/scratch/stefan/7916125/working/3D/233' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1)

`REAL250005043125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043125 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 43, 43, 43, 1, 48, 86, 86, 86, 86, 86, 48, 8, 8, 1, 1, 6, 43, 43, 43, 43, 1, 1, 86] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 16, 26, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35])
total number of confs: 284
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043125 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 133, 43, 43, 43, 43, 12, 43, 12, 1, 12, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 133, 133, 43, 43, 12, 1, 1, 1, 1, 43, 43, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 716
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043125 none O=C(NC[C@@H]1C[C@@H](NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 27, 86, 86, 86, 86, 86, 150, 150, 150, 201, 201, 201, 86, 1, 1, 1, 1, 1, 1, 5, 26, 26, 86, 86, 150, 201, 201, 201, 201, 86, 86, 1] 201
rigid atoms, others: [1, 35, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 631
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043125 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043125
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043125/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043125
Building REAL250005043126
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043126'
/scratch/stefan/7916125/working/building/REAL250005043126 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043126

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043126/0 /scratch/stefan/7916125/working/building/REAL250005043126 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/234
`/scratch/stefan/7916125/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043126 none O=C(CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens need 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, 44, 86, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 43, 54, 54, 54, 54, 54, 1, 44, 44, 86, 86, 6, 1, 1, 7, 7, 43, 54, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32])
total number of confs: 506
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043126 none O=C(CCF)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 5, 15, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [121, 121, 121, 201, 201, 54, 54, 54, 54, 18, 54, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 121, 54, 54, 17, 17, 4, 1, 54, 54] 201
rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 739
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043126 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043126
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043126/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043126
Building REAL250005043127
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043127'
/scratch/stefan/7916125/working/building/REAL250005043127 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043127

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043127/0 /scratch/stefan/7916125/working/building/REAL250005043127 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/235
`/scratch/stefan/7916125/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043127 none CO[C@H](C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 6, 51, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 41, 62, 62, 62, 62, 62, 1, 74, 74, 74, 51, 51, 51, 6, 1, 1, 7, 7, 41, 62, 1, 1] 201
rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 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, 33, 34, 35, 36])
total number of confs: 348
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043127 none CO[C@H](C)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 134, 201, 201, 134, 134, 62, 62, 62, 62, 23, 62, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 134, 62, 62, 22, 22, 3, 1, 62, 62] 201
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 736
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043127 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043127
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043127/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043127
Building REAL250005043128
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043128'
/scratch/stefan/7916125/working/building/REAL250005043128 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043128

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043128/0 /scratch/stefan/7916125/working/building/REAL250005043128 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/236
`/scratch/stefan/7916125/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043128 none C[C@@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [53, 6, 53, 53, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 51, 51, 51, 87, 87, 87, 87, 87, 1, 53, 53, 53, 159, 6, 1, 1, 9, 9, 51, 87, 1, 1] 549
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33])
total number of confs: 517
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043128 none C[C@@H](O)C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 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]
1  hydrogens need rotated
549  conformations in input
total number of sets (complete confs): 549
using faster count positions algorithm for large data
unique positions, atoms: [183, 156, 183, 183, 156, 156, 87, 87, 87, 87, 32, 87, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 87, 183, 183, 183, 549, 156, 87, 87, 32, 32, 6, 1, 87, 87] 549
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1181
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043128 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043128
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043128/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043128
Building REAL250005043129
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043129'
/scratch/stefan/7916125/working/building/REAL250005043129 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043129

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043129/0 /scratch/stefan/7916125/working/building/REAL250005043129 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/237
`/scratch/stefan/7916125/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043129 none C=C1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 54, 54, 54, 54, 54, 143, 201, 201, 201, 201, 201, 201, 201, 201, 54, 1, 1, 1, 1, 1, 13, 54, 54, 143, 143, 201, 201, 54, 54] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 735
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043129 none C=C1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [54, 54, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 74, 74, 74, 74, 74, 1, 54, 54, 54, 54, 54, 6, 1, 1, 9, 9, 47, 74, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 283
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043129 none C=C1CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 139, 139, 139, 74, 74, 74, 74, 28, 74, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 139, 74, 74, 27, 27, 5, 1, 74, 74] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 627
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043129 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043129
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043129/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043129
Building REAL250005043130
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043130'
/scratch/stefan/7916125/working/building/REAL250005043130 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043130

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043130/0 /scratch/stefan/7916125/working/building/REAL250005043130 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/238
`/scratch/stefan/7916125/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043130 none CC1=CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 13, 13, 13, 59, 59, 59, 59, 59, 146, 201, 201, 201, 201, 201, 201, 201, 201, 59, 2, 2, 2, 1, 1, 13, 59, 59, 146, 146, 201, 201, 59, 59] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 767
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043130 none CC1=CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [59, 59, 59, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 46, 46, 46, 68, 68, 68, 68, 68, 1, 59, 59, 59, 59, 59, 6, 1, 1, 7, 7, 46, 68, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34])
total number of confs: 281
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043130 none CC1=CC1C(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 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: [201, 201, 201, 132, 132, 132, 68, 68, 68, 68, 21, 68, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 132, 68, 68, 20, 20, 4, 1, 68, 68] 201
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 622
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043130 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043130
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043130/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043130
Building REAL250005043131
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043131'
/scratch/stefan/7916125/working/building/REAL250005043131 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043131

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043131/0 /scratch/stefan/7916125/working/building/REAL250005043131 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/239
`/scratch/stefan/7916125/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043131 none C=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 93, 93, 93, 93, 93, 1, 36, 36, 36, 6, 1, 1, 9, 9, 50, 93, 1, 1] 139
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 20, 25, 26, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 27, 28, 29, 30])
total number of confs: 278
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043131 none C=CC(=O)N[C@H]1C[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
139  conformations in input
total number of sets (complete confs): 139
using faster count positions algorithm for large data
unique positions, atoms: [139, 139, 139, 139, 93, 93, 93, 93, 40, 93, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 93, 139, 139, 139, 139, 93, 93, 39, 39, 6, 1, 93, 93] 139
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 441
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043131 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043131
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043131/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043131
Building REAL250005043132
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043132'
/scratch/stefan/7916125/working/building/REAL250005043132 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043132

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043132/0 /scratch/stefan/7916125/working/building/REAL250005043132 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/240
`/scratch/stefan/7916125/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043132 none CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [118, 47, 47, 47, 10, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 118, 118, 118, 118, 118, 47, 10, 10, 1, 1, 1, 1, 6, 22, 1, 1] 170
rigid atoms, others: [32, 33, 36, 5, 6, 7, 8, 9, 10, 11, 12, 21, 37, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 466
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043132 none CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [170, 139, 139, 139, 83, 22, 22, 22, 22, 22, 8, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 170, 170, 170, 170, 170, 139, 83, 83, 22, 22, 22, 22, 8, 1, 22, 22] 170
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 662
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043132 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043132
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043132/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043132
Building REAL250005043133
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043133'
/scratch/stefan/7916125/working/building/REAL250005043133 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043133

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043133/0 /scratch/stefan/7916125/working/building/REAL250005043133 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/241
`/scratch/stefan/7916125/working/3D/241' -> `0.mol2'
Preparing input files

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

`REAL250005043133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043133 none CC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 33, 33, 33, 33, 10, 10, 1, 1, 1, 1, 7, 18, 1, 1] 64
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 32, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 123
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043133 none CC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
64  conformations in input
total number of sets (complete confs): 64
using faster count positions algorithm for large data
unique positions, atoms: [64, 64, 64, 48, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 64, 64, 64, 64, 48, 48, 18, 18, 18, 18, 8, 1, 18, 18] 64
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 232
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043133 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043133
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043133/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043133
Building REAL250005043134
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043134'
/scratch/stefan/7916125/working/building/REAL250005043134 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043134

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043134/0 /scratch/stefan/7916125/working/building/REAL250005043134 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/242
`/scratch/stefan/7916125/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@@H]1CC[C@H](CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043134 none O=C(N[C@@H]1CC[C@H](CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 142, 142, 1, 7, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 10, 10, 50, 142, 142, 142, 142, 142, 1, 1, 18] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 16, 24, 25, 26, 27, 37, 36] set([0, 1, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 413
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043134 none O=C(N[C@@H]1CC[C@H](CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 142, 142, 142, 142, 142, 61, 142, 12, 12, 1, 12, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 142, 142, 142, 142, 61, 61, 12, 1, 1, 1, 1, 1, 142, 142, 201] 201
rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 661
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: REAL250005043134 none O=C(N[C@@H]1CC[C@H](CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 18, 18, 18, 18, 18, 18, 73, 154, 154, 154, 201, 201, 18, 1, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 73, 73, 154, 201, 201, 201, 201, 201, 18, 18, 1] 201
rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 669
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043134 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043134
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043134/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043134
Building REAL250005043135
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043135'
/scratch/stefan/7916125/working/building/REAL250005043135 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043135

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043135/0 /scratch/stefan/7916125/working/building/REAL250005043135 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/243
`/scratch/stefan/7916125/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043135 none COCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [133, 108, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 133, 133, 133, 108, 108, 43, 9, 9, 1, 1, 1, 1, 6, 20, 1, 1] 198
rigid atoms, others: [32, 33, 34, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 490
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043135 none COCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 157, 157, 157, 77, 20, 20, 20, 20, 20, 7, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 198, 198, 198, 198, 198, 157, 77, 77, 20, 20, 20, 20, 7, 1, 20, 20] 198
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043135 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043135
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043135/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043135
Building REAL250005043136
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043136'
/scratch/stefan/7916125/working/building/REAL250005043136 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043136

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043136/0 /scratch/stefan/7916125/working/building/REAL250005043136 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/244
`/scratch/stefan/7916125/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043136 none CCCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 132, 42, 42, 42, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 150, 150, 150, 150, 150, 132, 132, 42, 9, 9, 1, 1, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 635
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043136 none CCCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 116, 116, 116, 47, 13, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 198, 198, 116, 47, 47, 13, 13, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 776
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043136 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043136
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043136/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043136
Building REAL250005043137
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043137'
/scratch/stefan/7916125/working/building/REAL250005043137 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043137

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043137/0 /scratch/stefan/7916125/working/building/REAL250005043137 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/245
`/scratch/stefan/7916125/working/3D/245' -> `0.mol2'
Preparing input files

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

`REAL250005043137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043137 none CC(C)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [139, 45, 139, 45, 45, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 1, 139, 139, 139, 139, 139, 139, 139, 45, 10, 10, 1, 1, 1, 1, 7, 26, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 40, 22, 39] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 554
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043137 none CC(C)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 172, 201, 172, 172, 85, 26, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 201, 201, 172, 85, 85, 26, 26, 26, 26, 8, 1, 26, 26] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043137 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043137
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043137/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043137
Building REAL250005043138
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043138'
/scratch/stefan/7916125/working/building/REAL250005043138 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043138

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043138/0 /scratch/stefan/7916125/working/building/REAL250005043138 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/246
`/scratch/stefan/7916125/working/3D/246' -> `0.mol2'
Preparing input files

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

`REAL250005043138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043138 none NC(=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [81, 45, 84, 45, 45, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 1, 81, 84, 45, 9, 9, 1, 1, 1, 1, 7, 19, 1, 1] 142
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 14, 15, 16, 17, 18, 19, 20, 21, 33, 23, 24, 25, 26, 27])
total number of confs: 268
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043138 none NC(=O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [140, 131, 142, 131, 131, 71, 19, 19, 19, 19, 19, 6, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 140, 142, 131, 71, 71, 19, 19, 19, 19, 7, 1, 19, 19] 142
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 497
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043138 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043138
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043138/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043138
Building REAL250005043139
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043139'
/scratch/stefan/7916125/working/building/REAL250005043139 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043139

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043139/0 /scratch/stefan/7916125/working/building/REAL250005043139 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/247
`/scratch/stefan/7916125/working/3D/247' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043139 none C=CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 99, 30, 30, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 1, 157, 157, 157, 99, 99, 30, 7, 7, 1, 1, 1, 1, 7, 26, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 591
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043139 none C=CCC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 142, 142, 142, 70, 26, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 201, 201, 201, 201, 201, 142, 70, 70, 26, 26, 26, 26, 8, 1, 26, 26] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 795
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043139 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043139
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043139/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043139
Building REAL250005043140
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043140'
/scratch/stefan/7916125/working/building/REAL250005043140 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043140

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043140/0 /scratch/stefan/7916125/working/building/REAL250005043140 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/248
`/scratch/stefan/7916125/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043140 none O=C(CO)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
333  conformations in input
total number of sets (complete confs): 333
using faster count positions algorithm for large data
unique positions, atoms: [42, 42, 42, 78, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 1, 78, 78, 234, 42, 10, 10, 1, 1, 1, 1, 7, 18, 1, 1] 333
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27])
total number of confs: 549
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043140 none O=C(CO)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
333  conformations in input
total number of sets (complete confs): 333
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 108, 111, 62, 18, 18, 18, 18, 18, 8, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 111, 111, 333, 108, 62, 62, 18, 18, 18, 18, 8, 1, 18, 18] 333
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 724
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043140 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043140
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043140/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043140
Building REAL250005043141
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043141'
/scratch/stefan/7916125/working/building/REAL250005043141 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043141

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043141/0 /scratch/stefan/7916125/working/building/REAL250005043141 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/249
`/scratch/stefan/7916125/working/3D/249' -> `0.mol2'
Preparing input files

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

`REAL250005043141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043141 none CC(O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
573  conformations in input
total number of sets (complete confs): 573
using faster count positions algorithm for large data
unique positions, atoms: [141, 46, 140, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 1, 141, 141, 141, 141, 423, 46, 10, 10, 1, 1, 1, 1, 7, 26, 1, 1] 573
rigid atoms, others: [32, 33, 34, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 972
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043141 none CC(O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
573  conformations in input
total number of sets (complete confs): 573
using faster count positions algorithm for large data
unique positions, atoms: [191, 172, 191, 172, 172, 86, 26, 26, 26, 26, 26, 7, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 191, 191, 191, 191, 573, 172, 86, 86, 26, 26, 26, 26, 8, 1, 26, 26] 573
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1256
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043141 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043141
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043141/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043141
Building REAL250005043142
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043142'
/scratch/stefan/7916125/working/building/REAL250005043142 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043142

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043142/0 /scratch/stefan/7916125/working/building/REAL250005043142 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/250
`/scratch/stefan/7916125/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043142 none O=C(CCF)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 132, 153, 9, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 132, 132, 153, 153, 41, 9, 9, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 612
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043142 none O=C(CCF)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 106, 201, 201, 44, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 106, 44, 44, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 760
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043142 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043142
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043142/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043142
Building REAL250005043143
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043143'
/scratch/stefan/7916125/working/building/REAL250005043143 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043143

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043143/0 /scratch/stefan/7916125/working/building/REAL250005043143 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/251
`/scratch/stefan/7916125/working/3D/251' -> `0.mol2'
Preparing input files

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

`REAL250005043143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043143 none C[C@@H](O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
516  conformations in input
total number of sets (complete confs): 516
using faster count positions algorithm for large data
unique positions, atoms: [119, 46, 119, 116, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 1, 119, 119, 119, 357, 46, 10, 10, 1, 1, 1, 1, 7, 26, 1, 1] 516
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 824
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043143 none C[C@@H](O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
516  conformations in input
total number of sets (complete confs): 516
using faster count positions algorithm for large data
unique positions, atoms: [172, 146, 172, 172, 146, 146, 83, 26, 26, 26, 26, 26, 8, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 172, 172, 172, 516, 146, 83, 83, 26, 26, 26, 26, 8, 1, 26, 26] 516
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043143 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043143
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043143/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043143
Building REAL250005043144
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043144'
/scratch/stefan/7916125/working/building/REAL250005043144 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043144

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043144/0 /scratch/stefan/7916125/working/building/REAL250005043144 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/252
`/scratch/stefan/7916125/working/3D/252' -> `0.mol2'
Preparing input files

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

`REAL250005043144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043144 none C[C@H](O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
519  conformations in input
total number of sets (complete confs): 519
using faster count positions algorithm for large data
unique positions, atoms: [133, 46, 133, 133, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 1, 133, 133, 133, 399, 46, 10, 10, 1, 1, 1, 1, 7, 28, 1, 1] 519
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 930
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043144 none C[C@H](O)C(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
519  conformations in input
total number of sets (complete confs): 519
using faster count positions algorithm for large data
unique positions, atoms: [173, 153, 173, 173, 153, 153, 84, 28, 28, 28, 28, 28, 8, 28, 8, 1, 8, 1, 1, 1, 1, 1, 1, 28, 173, 173, 173, 519, 153, 84, 84, 28, 28, 28, 28, 8, 1, 28, 28] 519
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1157
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043144 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043144
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043144/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043144
Building REAL250005043145
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043145'
/scratch/stefan/7916125/working/building/REAL250005043145 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043145

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043145/0 /scratch/stefan/7916125/working/building/REAL250005043145 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/253
`/scratch/stefan/7916125/working/3D/253' -> `0.mol2'
Preparing input files

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

`REAL250005043145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043145 none CC=CC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [116, 116, 46, 46, 46, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 1, 116, 116, 116, 116, 116, 46, 10, 10, 1, 1, 1, 1, 7, 25, 1, 1] 170
rigid atoms, others: [32, 33, 34, 37, 6, 7, 8, 9, 10, 11, 12, 13, 22, 38, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 368
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043145 none CC=CC(=O)NC[C@H]1CC[C@@H](NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
170  conformations in input
total number of sets (complete confs): 170
using faster count positions algorithm for large data
unique positions, atoms: [170, 170, 141, 141, 141, 81, 25, 25, 25, 25, 25, 7, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 170, 170, 170, 170, 170, 141, 81, 81, 25, 25, 25, 25, 8, 1, 25, 25] 170
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 608
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043145 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043145
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043145/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043145
Building REAL250005043146
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043146'
/scratch/stefan/7916125/working/building/REAL250005043146 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043146

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043146/0 /scratch/stefan/7916125/working/building/REAL250005043146 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/254
`/scratch/stefan/7916125/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043146 none COCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 43, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 56, 56, 56, 56, 56, 1, 72, 72, 72, 43, 43, 6, 1, 1, 1, 1, 10, 10, 45, 56, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 37, 22, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 324
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043146 none COCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 131, 131, 131, 56, 56, 56, 56, 56, 16, 56, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 131, 56, 56, 56, 56, 16, 16, 4, 1, 56, 56] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 734
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043146 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043146
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043146/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043146
Building REAL250005043147
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043147'
/scratch/stefan/7916125/working/building/REAL250005043147 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043147

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043147/0 /scratch/stefan/7916125/working/building/REAL250005043147 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/255
`/scratch/stefan/7916125/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043147 none CCCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 44, 44, 44, 50, 50, 50, 50, 50, 1, 58, 58, 58, 58, 58, 41, 41, 6, 1, 1, 1, 1, 8, 8, 44, 50, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 412
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043147 none CCCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 112, 112, 112, 50, 50, 50, 50, 50, 16, 50, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 112, 50, 50, 50, 50, 16, 16, 4, 1, 50, 50] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 781
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043147 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043147
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043147/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043147
Building REAL250005043148
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043148'
/scratch/stefan/7916125/working/building/REAL250005043148 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043148

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043148/0 /scratch/stefan/7916125/working/building/REAL250005043148 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/256
`/scratch/stefan/7916125/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043148 none CC(C)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [39, 7, 39, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 57, 57, 57, 100, 100, 100, 100, 100, 1, 39, 39, 39, 39, 39, 39, 39, 7, 1, 1, 1, 1, 10, 10, 57, 100, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 346
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043148 none CC(C)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 175, 201, 175, 175, 100, 100, 100, 100, 100, 32, 100, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 175, 100, 100, 100, 100, 32, 32, 6, 1, 100, 100] 201
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 702
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043148 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043148
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043148/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043148
Building REAL250005043149
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043149'
/scratch/stefan/7916125/working/building/REAL250005043149 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043149

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043149/0 /scratch/stefan/7916125/working/building/REAL250005043149 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/257
`/scratch/stefan/7916125/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043149 none CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 100, 100, 100, 100, 100, 1, 51, 51, 51, 51, 51, 7, 1, 1, 1, 1, 10, 10, 54, 100, 1, 1] 201
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 37, 21, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 379
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043149 none CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 164, 100, 100, 100, 100, 100, 38, 100, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 164, 100, 100, 100, 100, 37, 37, 7, 1, 100, 100] 201
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 751
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043149 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043149
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043149/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043149
Building REAL250005043150
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043150'
/scratch/stefan/7916125/working/building/REAL250005043150 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043150

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043150/0 /scratch/stefan/7916125/working/building/REAL250005043150 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/258
`/scratch/stefan/7916125/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043150 none CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 41, 41, 41, 61, 61, 61, 61, 61, 1, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 41, 61, 1, 1] 73
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 20, 25, 26, 27, 28] set([0, 1, 2, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 157
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043150 none CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 61, 61, 61, 61, 61, 36, 61, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 61, 73, 73, 73, 73, 61, 61, 61, 61, 36, 36, 8, 1, 61, 61] 73
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 246
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043150 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043150
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043150/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043150
Building REAL250005043151
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043151'
/scratch/stefan/7916125/working/building/REAL250005043151 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043151

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043151/0 /scratch/stefan/7916125/working/building/REAL250005043151 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/259
`/scratch/stefan/7916125/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC[C@H]1CC[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043151 none O=C(NC[C@H]1CC[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 46, 46, 1, 53, 79, 79, 79, 79, 79, 53, 10, 10, 1, 1, 1, 1, 7, 46, 46, 46, 46, 46, 1, 1, 79] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 16, 36, 26, 27, 28, 29, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 288
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043151 none O=C(NC[C@H]1CC[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 131, 47, 47, 47, 47, 47, 12, 47, 12, 1, 12, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 131, 131, 47, 47, 47, 47, 12, 1, 1, 1, 1, 1, 47, 47, 201] 201
rigid atoms, others: [32, 33, 34, 35, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 685
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: REAL250005043151 none O=C(NC[C@H]1CC[C@@H](NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 26, 80, 80, 80, 80, 80, 80, 143, 143, 143, 201, 201, 80, 1, 1, 1, 1, 1, 1, 5, 26, 26, 80, 80, 80, 80, 143, 201, 201, 201, 201, 201, 80, 80, 1] 201
rigid atoms, others: [1, 38, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 650
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043151 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043151
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043151/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043151
Building REAL250005043152
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043152'
/scratch/stefan/7916125/working/building/REAL250005043152 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043152

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043152/0 /scratch/stefan/7916125/working/building/REAL250005043152 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/260
`/scratch/stefan/7916125/working/3D/260' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043152 none NC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [24, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 29, 29, 29, 29, 29, 1, 24, 25, 6, 1, 1, 1, 1, 9, 9, 25, 29, 1, 1] 69
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 22, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 143
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043152 none NC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [68, 49, 69, 49, 49, 29, 29, 29, 29, 29, 13, 29, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 29, 68, 69, 49, 29, 29, 29, 29, 12, 12, 3, 1, 29, 29] 69
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043152 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043152
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043152/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043152
Building REAL250005043153
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043153'
/scratch/stefan/7916125/working/building/REAL250005043153 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043153

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043153/0 /scratch/stefan/7916125/working/building/REAL250005043153 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/261
`/scratch/stefan/7916125/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043153 none O=C(CO)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
408  conformations in input
total number of sets (complete confs): 408
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 46, 1, 1, 1, 1, 1, 1, 1, 1, 10, 52, 52, 52, 75, 75, 75, 75, 75, 1, 46, 46, 138, 7, 1, 1, 1, 1, 10, 10, 52, 75, 1, 1] 408
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31])
total number of confs: 460
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043153 none O=C(CO)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
408  conformations in input
total number of sets (complete confs): 408
using faster count positions algorithm for large data
unique positions, atoms: [120, 120, 120, 136, 75, 75, 75, 75, 75, 26, 75, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 75, 136, 136, 408, 120, 75, 75, 75, 75, 26, 26, 6, 1, 75, 75] 408
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 873
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043153 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043153
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043153/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043153
Building REAL250005043154
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043154'
/scratch/stefan/7916125/working/building/REAL250005043154 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043154

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043154/0 /scratch/stefan/7916125/working/building/REAL250005043154 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/262
`/scratch/stefan/7916125/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043154 none CC(O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [48, 6, 48, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 43, 43, 43, 65, 65, 65, 65, 65, 1, 48, 48, 48, 48, 144, 6, 1, 1, 1, 1, 10, 10, 43, 65, 1, 1] 531
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 37, 22, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 447
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043154 none CC(O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 140, 177, 140, 140, 65, 65, 65, 65, 65, 23, 65, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 65, 177, 177, 177, 177, 531, 140, 65, 65, 65, 65, 22, 22, 5, 1, 65, 65] 531
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1161
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043154 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043154
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043154/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043154
Building REAL250005043155
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043155'
/scratch/stefan/7916125/working/building/REAL250005043155 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043155

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043155/0 /scratch/stefan/7916125/working/building/REAL250005043155 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/263
`/scratch/stefan/7916125/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043155 none CC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [37, 6, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 49, 49, 49, 49, 49, 1, 37, 37, 37, 6, 1, 1, 1, 1, 9, 9, 40, 49, 1, 1] 130
rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 22, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 207
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043155 none CC(=O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 106, 130, 106, 106, 49, 49, 49, 49, 49, 21, 49, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 49, 130, 130, 130, 106, 49, 49, 49, 49, 20, 20, 3, 1, 49, 49] 130
rigid atoms, others: [34, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 408
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043155 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043155
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043155/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043155
Building REAL250005043156
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043156'
/scratch/stefan/7916125/working/building/REAL250005043156 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043156

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043156/0 /scratch/stefan/7916125/working/building/REAL250005043156 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/264
`/scratch/stefan/7916125/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043156 none CC=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 53, 53, 53, 103, 103, 103, 103, 103, 1, 39, 39, 39, 39, 39, 7, 1, 1, 1, 1, 10, 10, 53, 103, 1, 1] 176
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 37, 22, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 303
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043156 none CC=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [176, 176, 147, 147, 147, 103, 103, 103, 103, 103, 43, 103, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 103, 176, 176, 176, 176, 176, 147, 103, 103, 103, 103, 42, 42, 7, 1, 103, 103] 176
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 581
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043156 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043156
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043156/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043156
Building REAL250005043157
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043157'
/scratch/stefan/7916125/working/building/REAL250005043157 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043157

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043157/0 /scratch/stefan/7916125/working/building/REAL250005043157 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/265
`/scratch/stefan/7916125/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043157 none C[C@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
534  conformations in input
total number of sets (complete confs): 534
using faster count positions algorithm for large data
unique positions, atoms: [48, 6, 48, 48, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 66, 66, 66, 66, 66, 1, 48, 48, 48, 144, 6, 1, 1, 1, 1, 10, 10, 45, 66, 1, 1] 534
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 13, 23, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 449
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043157 none C[C@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
534  conformations in input
total number of sets (complete confs): 534
using faster count positions algorithm for large data
unique positions, atoms: [178, 140, 178, 178, 140, 140, 66, 66, 66, 66, 66, 24, 66, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 66, 178, 178, 178, 534, 140, 66, 66, 66, 66, 23, 23, 5, 1, 66, 66] 534
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1171
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043157 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043157
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043157/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043157
Building REAL250005043158
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043158'
/scratch/stefan/7916125/working/building/REAL250005043158 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043158

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043158/0 /scratch/stefan/7916125/working/building/REAL250005043158 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/266
`/scratch/stefan/7916125/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043158 none C=CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 39, 39, 39, 51, 51, 51, 51, 51, 1, 92, 92, 92, 45, 45, 6, 1, 1, 1, 1, 8, 8, 39, 51, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 37, 22, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 421
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043158 none C=CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 118, 118, 118, 51, 51, 51, 51, 51, 18, 51, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 118, 51, 51, 51, 51, 18, 18, 4, 1, 51, 51] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 755
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043158 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043158
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043158/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043158
Building REAL250005043159
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043159'
/scratch/stefan/7916125/working/building/REAL250005043159 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043159

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043159/0 /scratch/stefan/7916125/working/building/REAL250005043159 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/267
`/scratch/stefan/7916125/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043159 none N#CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 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: [54, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 48, 48, 48, 68, 68, 68, 68, 68, 1, 54, 54, 6, 1, 1, 1, 1, 10, 10, 48, 68, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 22, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 33, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043159 none N#CCC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 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, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 145, 145, 145, 68, 68, 68, 68, 68, 23, 68, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 68, 201, 201, 145, 68, 68, 68, 68, 23, 23, 4, 1, 68, 68] 201
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043159 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043159
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043159/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043159
Building REAL250005043160
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043160'
/scratch/stefan/7916125/working/building/REAL250005043160 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043160

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043160/0 /scratch/stefan/7916125/working/building/REAL250005043160 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/268
`/scratch/stefan/7916125/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043160 none O=C(CCF)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 31, 52, 1, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 46, 54, 54, 54, 54, 54, 1, 31, 31, 52, 52, 6, 1, 1, 1, 1, 9, 9, 46, 54, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 12, 37, 22, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 350
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043160 none O=C(CCF)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 201, 201, 54, 54, 54, 54, 54, 17, 54, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 97, 54, 54, 54, 54, 16, 16, 4, 1, 54, 54] 201
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 751
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043160 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043160
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043160/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043160
Building REAL250005043161
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043161'
/scratch/stefan/7916125/working/building/REAL250005043161 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043161

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043161/0 /scratch/stefan/7916125/working/building/REAL250005043161 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/269
`/scratch/stefan/7916125/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043161 none C[C@@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 51, 51, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 59, 59, 59, 84, 84, 84, 84, 84, 1, 51, 51, 51, 153, 7, 1, 1, 1, 1, 10, 10, 59, 84, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 11, 12, 13, 23, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 510
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043161 none C[C@@H](O)C(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 160, 201, 201, 160, 160, 84, 84, 84, 84, 84, 24, 84, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 603, 160, 84, 84, 84, 84, 23, 23, 3, 1, 84, 84] 603
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1313
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043161 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043161
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043161/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043161
Building REAL250005043162
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043162'
/scratch/stefan/7916125/working/building/REAL250005043162 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043162

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043162/0 /scratch/stefan/7916125/working/building/REAL250005043162 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/270
`/scratch/stefan/7916125/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043162 none C=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 53, 53, 53, 99, 99, 99, 99, 99, 1, 28, 28, 28, 7, 1, 1, 1, 1, 10, 10, 53, 99, 1, 1] 146
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 21, 26, 27, 28, 29] set([0, 1, 2, 3, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 30, 31])
total number of confs: 276
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043162 none C=CC(=O)N[C@@H]1CC[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [146, 146, 146, 146, 99, 99, 99, 99, 99, 43, 99, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 99, 146, 146, 146, 146, 99, 99, 99, 99, 42, 42, 7, 1, 99, 99] 146
rigid atoms, others: [33, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 461
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043162 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043162
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043162/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043162
Building REAL250005043163
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043163'
/scratch/stefan/7916125/working/building/REAL250005043163 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043163

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043163/0 /scratch/stefan/7916125/working/building/REAL250005043163 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/271
`/scratch/stefan/7916125/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCC(C)C1CCNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043163 none CC(=O)N1CCCC(C)C1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 14, 14, 14, 18, 18, 18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 3, 3, 5, 5, 14, 18] 18
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 65
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043163 none CC(=O)N1CCCC(C)C1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 14, 14, 7, 1] 18
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 66
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043163 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043163
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043163/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043163
Building REAL250005043164
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043164'
/scratch/stefan/7916125/working/building/REAL250005043164 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043164

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043164/0 /scratch/stefan/7916125/working/building/REAL250005043164 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/272
`/scratch/stefan/7916125/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043164 none CC(=O)NCCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 11, 11, 11, 11, 5, 5, 4, 4, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12] 18
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 39, 38, 29, 30, 37] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 40])
total number of confs: 62
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043164 none CC(=O)NCCC1C(C)CCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 14, 12, 12, 12, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 16, 16, 14, 14, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 18
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 57
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043164 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043164
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043164/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043164
Building REAL250005043165
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043165'
/scratch/stefan/7916125/working/building/REAL250005043165 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043165

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043165/0 /scratch/stefan/7916125/working/building/REAL250005043165 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/273
`/scratch/stefan/7916125/working/3D/273' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCO[C@@H]1CN(C(C)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043165 none CCO[C@@H]1CN(C(C)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 5, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 9, 37, 37, 37, 48, 48, 48, 48, 48, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 1, 1, 9, 9, 37, 48] 73
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 10, 11, 12, 34, 13, 28, 29] set([0, 1, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 155
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043165 none CCO[C@@H]1CN(C(C)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 5, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 48, 48, 48, 48, 48, 48, 71, 71, 48, 22, 48, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 71, 71, 71, 48, 48, 22, 22, 8, 1] 73
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 237
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043165 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043165
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043165/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043165
Building REAL250005043166
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043166'
/scratch/stefan/7916125/working/building/REAL250005043166 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043166

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043166/0 /scratch/stefan/7916125/working/building/REAL250005043166 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/274
`/scratch/stefan/7916125/working/3D/274' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(C)=O)

`REAL250005043166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043166 none CCO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 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: [6, 5, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 1, 9, 38, 38, 38, 6, 6, 6, 6, 6, 1, 1, 25, 1, 1, 9, 9, 38, 38, 38, 38] 119
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 28, 29, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 146
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043166 none CCO[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 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: [48, 45, 25, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 80, 117, 117, 117, 48, 48, 48, 48, 48, 25, 25, 1, 25, 25, 80, 80, 117, 117, 117, 117] 119
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 449
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043166 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043166
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043166/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043166
Building REAL250005043167
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043167'
/scratch/stefan/7916125/working/building/REAL250005043167 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043167

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043167/0 /scratch/stefan/7916125/working/building/REAL250005043167 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/275
`/scratch/stefan/7916125/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043167 none CCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 17, 27] 32
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 36, 28, 29, 30, 31] set([0, 1, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 105
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043167 none CCC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 30, 27, 30, 27, 27, 27, 27, 27, 27, 27, 16, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 6, 1] 32
rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 116
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043167 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043167
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043167/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043167
Building REAL250005043168
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043168'
/scratch/stefan/7916125/working/building/REAL250005043168 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043168

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043168/0 /scratch/stefan/7916125/working/building/REAL250005043168 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/276
`/scratch/stefan/7916125/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043168 none CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 19, 19, 19, 19, 19, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 17, 19] 19
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 33, 25, 26, 27, 28] set([0, 35, 2, 34, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31])
total number of confs: 64
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043168 none CC(=O)N1CC[C@@H](C)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 7, 1] 19
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 66
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043168 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043168
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043168/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043168
Building REAL250005043169
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043169'
/scratch/stefan/7916125/working/building/REAL250005043169 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043169

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043169/0 /scratch/stefan/7916125/working/building/REAL250005043169 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/277
`/scratch/stefan/7916125/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CCN(C(=O)CO)[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043169 none C[C@@H]1CCN(C(=O)CO)[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 1, 1, 1, 7, 21, 21, 21, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 30, 7, 7, 21, 30, 1, 1] 123
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31])
total number of confs: 133
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043169 none C[C@@H]1CCN(C(=O)CO)[C@H](CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 35, 35, 41, 19, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 41, 41, 123, 19, 19, 8, 1, 30, 30] 123
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 277
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043169 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043169
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043169/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043169
Building REAL250005043170
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043170'
/scratch/stefan/7916125/working/building/REAL250005043170 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043170

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043170/0 /scratch/stefan/7916125/working/building/REAL250005043170 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/278
`/scratch/stefan/7916125/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043170 none CCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 21, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 40, 40, 40, 40, 40, 21, 8, 8, 1, 1, 2, 2, 2, 1, 1, 1, 1, 14] 54
rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 39, 38, 37, 31] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 40])
total number of confs: 176
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043170 none CCC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 40, 40, 40, 27, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 40, 27, 27, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 54
rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 224
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043170 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043170
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043170/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043170
Building REAL250005043171
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043171'
/scratch/stefan/7916125/working/building/REAL250005043171 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043171

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043171/0 /scratch/stefan/7916125/working/building/REAL250005043171 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/279
`/scratch/stefan/7916125/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043171 none CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 14, 14, 14, 14, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 11] 23
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 28, 29] set([0, 1, 2, 3, 37, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31])
total number of confs: 66
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043171 none CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 21, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 21, 21, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 23
rigid atoms, others: [37, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 79
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043171 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043171
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043171/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043171
Building REAL250005043172
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043172'
/scratch/stefan/7916125/working/building/REAL250005043172 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043172

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043172/0 /scratch/stefan/7916125/working/building/REAL250005043172 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/280
`/scratch/stefan/7916125/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@H](CNC(=O)CO)C1)

`REAL250005043172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043172 none C[C@@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@H](CNC(=O)CO)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 8, 16, 16, 16, 28, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 28, 28, 84, 1, 1] 90
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 30, 31])
total number of confs: 198
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043172 none C[C@@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@H](CNC(=O)CO)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 24, 24, 24, 30, 8, 8, 8, 8, 8, 8, 8, 8, 1, 14, 14, 24, 30, 30, 90, 8, 8] 90
rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 197
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043172 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043172
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043172/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043172
Building REAL250005043173
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043173'
/scratch/stefan/7916125/working/building/REAL250005043173 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043173

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043173/0 /scratch/stefan/7916125/working/building/REAL250005043173 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/281
`/scratch/stefan/7916125/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043173 none C=CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [26, 20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 12, 12, 12, 12, 26, 26, 26, 20, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12] 38
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 37] set([0, 1, 2, 3, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 38])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043173 none C=CC(=O)NC[C@@H]1C[C@H](C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 38, 38, 38, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1] 38
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 130
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043173 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043173
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043173/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043173
Building REAL250005043174
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043174'
/scratch/stefan/7916125/working/building/REAL250005043174 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043174

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043174/0 /scratch/stefan/7916125/working/building/REAL250005043174 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/282
`/scratch/stefan/7916125/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)CCCCCCNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043174 none CCC(=O)N(C)CCCCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 135, 197, 84, 135, 54, 33, 32, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 135, 135, 86, 86, 55, 55, 44, 44, 30, 30, 24, 24, 10, 10, 2, 1] 201
rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 929
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043174 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043174
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043174/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043174
Building REAL250005043175
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043175'
/scratch/stefan/7916125/working/building/REAL250005043175 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043175

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043175/0 /scratch/stefan/7916125/working/building/REAL250005043175 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/283
`/scratch/stefan/7916125/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CCCCCCNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043175 none CC(=O)N(C)CCCCCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 187, 201, 132, 187, 79, 49, 40, 21, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 187, 187, 134, 134, 86, 86, 66, 66, 40, 40, 28, 28, 16, 16, 4, 1] 201
rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 1025
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043175 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043175
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043175/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043175
Building REAL250005043176
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043176'
/scratch/stefan/7916125/working/building/REAL250005043176 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043176

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043176/0 /scratch/stefan/7916125/working/building/REAL250005043176 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/284
`/scratch/stefan/7916125/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CCCCCCNC(=O)C1=CC(=O)[N-]O1)C(=O)CO)

`REAL250005043176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043176 none CN(CCCCCCNC(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.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, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [137, 71, 45, 27, 30, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 137, 199, 199, 201, 137, 137, 137, 72, 72, 46, 46, 38, 38, 28, 28, 24, 24, 10, 10, 2, 1, 201, 201, 603] 603
rigid atoms, others: [37, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 1488
number of broken/clashed sets: 106
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043176 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043176
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043176/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043176
Building REAL250005043177
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043177'
/scratch/stefan/7916125/working/building/REAL250005043177 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043177

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043177/0 /scratch/stefan/7916125/working/building/REAL250005043177 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/285
`/scratch/stefan/7916125/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043177 none CCC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 69, 31, 29, 31, 29, 25, 11, 5, 11, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 69, 69, 31, 31, 31, 31, 31, 31, 31, 31, 25, 25, 11, 11, 11, 1] 201
rigid atoms, others: [42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 1014
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043177 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043177
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043177/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043177
Building REAL250005043178
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043178'
/scratch/stefan/7916125/working/building/REAL250005043178 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043178

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043178/0 /scratch/stefan/7916125/working/building/REAL250005043178 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/286
`/scratch/stefan/7916125/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043178 none CC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 73, 62, 56, 40, 36, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 134, 134, 75, 75, 66, 66, 55, 55, 44, 44, 36, 36, 15, 15, 15, 1] 201
rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 922
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043178 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043178
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043178/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043178
Building REAL250005043179
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043179'
/scratch/stefan/7916125/working/building/REAL250005043179 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043179

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043179/0 /scratch/stefan/7916125/working/building/REAL250005043179 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/287
`/scratch/stefan/7916125/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CCCCCCNC(=O)CO)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043179 none CN(CCCCCCNC(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [13, 6, 13, 31, 35, 43, 45, 48, 98, 201, 201, 201, 201, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 31, 31, 37, 37, 43, 43, 47, 47, 50, 50, 97, 97, 201, 201, 201, 603, 1] 603
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 1454
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043179 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043179
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043179/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043179
Building REAL250005043180
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043180'
/scratch/stefan/7916125/working/building/REAL250005043180 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043180

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043180/0 /scratch/stefan/7916125/working/building/REAL250005043180 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/288
`/scratch/stefan/7916125/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043180 none C=CC(=O)NCCCCCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 97, 42, 38, 42, 38, 33, 13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 97, 97, 42, 42, 42, 42, 42, 42, 42, 42, 33, 33, 13, 13, 13, 1] 201
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 808
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043180 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043180
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043180/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043180
Building REAL250005043181
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043181'
/scratch/stefan/7916125/working/building/REAL250005043181 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043181

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043181/0 /scratch/stefan/7916125/working/building/REAL250005043181 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/289
`/scratch/stefan/7916125/working/3D/289' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC)

`REAL250005043181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043181 none CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 3, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 27, 3, 3, 3, 3, 3] 89
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37])
total number of confs: 144
number of broken/clashed sets: 88
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043181 none CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [65, 47, 47, 47, 27, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 42, 65, 65, 65, 65, 65, 47, 27, 27, 27, 27, 1, 42, 42, 42, 42, 42] 89
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 299
number of broken/clashed sets: 88
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043181 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043181
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043181/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043181
Building REAL250005043182
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043182'
/scratch/stefan/7916125/working/building/REAL250005043182 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043182

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043182/0 /scratch/stefan/7916125/working/building/REAL250005043182 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/290
`/scratch/stefan/7916125/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(C)=O)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043182 none CC[C@@H]1[C@@H](NC(C)=O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 5, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 6, 6, 6, 6, 1, 1, 1, 1, 17] 28
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 13, 30, 31] set([0, 34, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 49
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043182 none CC[C@@H]1[C@@H](NC(C)=O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 5, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [25, 17, 17, 17, 17, 17, 17, 20, 20, 20, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 20, 20, 20, 20, 17, 17, 17, 17, 1] 28
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 91
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043182 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043182
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043182/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043182
Building REAL250005043183
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043183'
/scratch/stefan/7916125/working/building/REAL250005043183 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043183

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043183/0 /scratch/stefan/7916125/working/building/REAL250005043183 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/291
`/scratch/stefan/7916125/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2CC2)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043183 none CC[C@@H]1[C@@H](NC(=O)C2CC2)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 36, 36, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 6, 36, 36, 36, 36, 36, 1, 1, 1, 1, 26] 114
rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 34, 35, 36, 37] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 129
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043183 none CC[C@@H]1[C@@H](NC(=O)C2CC2)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [55, 36, 36, 36, 12, 36, 12, 1, 12, 1, 1, 1, 36, 36, 36, 36, 80, 80, 111, 111, 111, 111, 111, 55, 55, 55, 55, 55, 12, 1, 1, 1, 1, 1, 36, 36, 36, 36, 111] 114
rigid atoms, others: [32, 33, 7, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 394
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: REAL250005043183 none CC[C@@H]1[C@@H](NC(=O)C2CC2)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [41, 26, 26, 26, 26, 26, 26, 62, 62, 62, 111, 111, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 62, 111, 111, 111, 111, 111, 26, 26, 26, 26, 1] 114
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 398
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043183 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043183
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043183/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043183
Building REAL250005043184
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043184'
/scratch/stefan/7916125/working/building/REAL250005043184 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043184

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043184/0 /scratch/stefan/7916125/working/building/REAL250005043184 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/292
`/scratch/stefan/7916125/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)COC)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043184 none CC[C@@H]1[C@@H](NC(=O)COC)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 68, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 6, 41, 41, 68, 68, 68, 1, 1, 1, 1, 21] 120
rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 34, 35, 36, 37] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 219
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043184 none CC[C@@H]1[C@@H](NC(=O)COC)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [34, 21, 21, 21, 21, 21, 21, 59, 59, 59, 112, 115, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 59, 112, 112, 115, 115, 115, 21, 21, 21, 21, 1] 120
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 460
number of broken/clashed sets: 81
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043184 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043184
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043184/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043184
Building REAL250005043185
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043185'
/scratch/stefan/7916125/working/building/REAL250005043185 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043185

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043185/0 /scratch/stefan/7916125/working/building/REAL250005043185 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/293
`/scratch/stefan/7916125/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC)

`REAL250005043185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043185 none CCCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [54, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 1, 3, 67, 67, 67, 67, 67, 41, 41, 6, 1, 1, 1, 1, 25, 3, 3, 3, 3, 3] 194
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 395
number of broken/clashed sets: 193
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043185 none CCCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [181, 174, 70, 70, 70, 25, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 39, 185, 185, 185, 185, 185, 174, 174, 70, 25, 25, 25, 25, 1, 39, 39, 39, 39, 39] 194
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 803
number of broken/clashed sets: 193
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043185 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043185
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043185/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043185
Building REAL250005043186
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043186'
/scratch/stefan/7916125/working/building/REAL250005043186 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043186

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043186/0 /scratch/stefan/7916125/working/building/REAL250005043186 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/294
`/scratch/stefan/7916125/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C(C)C)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043186 none CC[C@@H]1[C@@H](NC(=O)C(C)C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 31, 31, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 6, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 26] 105
rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 12, 13, 14, 15, 36, 38, 37] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40])
total number of confs: 149
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043186 none CC[C@@H]1[C@@H](NC(=O)C(C)C)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [43, 26, 26, 26, 26, 26, 26, 67, 67, 67, 96, 96, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 67, 96, 96, 96, 96, 96, 96, 96, 26, 26, 26, 26, 1] 105
rigid atoms, others: [40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 423
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043186 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043186
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043186/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043186
Building REAL250005043187
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043187'
/scratch/stefan/7916125/working/building/REAL250005043187 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043187

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043187/0 /scratch/stefan/7916125/working/building/REAL250005043187 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/295
`/scratch/stefan/7916125/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C(N)=O)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043187 none CC[C@@H]1[C@@H](NC(=O)C(N)=O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 6, 15, 15, 1, 1, 1, 1, 18] 38
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 12, 13, 14, 15, 34, 31] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 77
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043187 none CC[C@@H]1[C@@H](NC(=O)C(N)=O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 8, 11, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [22, 18, 18, 18, 18, 18, 18, 31, 31, 31, 36, 36, 18, 18, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 31, 36, 36, 18, 18, 18, 18, 1] 38
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 116
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043187 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043187
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043187/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043187
Building REAL250005043188
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043188'
/scratch/stefan/7916125/working/building/REAL250005043188 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043188

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043188/0 /scratch/stefan/7916125/working/building/REAL250005043188 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/296
`/scratch/stefan/7916125/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC)

`REAL250005043188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043188 none C=CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 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
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [52, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 1, 1, 1, 3, 52, 52, 52, 30, 30, 6, 1, 1, 1, 1, 27, 3, 3, 3, 3, 3] 99
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 216
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043188 none C=CCC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 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
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [95, 94, 52, 52, 52, 27, 27, 27, 27, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 27, 34, 95, 95, 95, 94, 94, 52, 27, 27, 27, 27, 1, 34, 34, 34, 34, 34] 99
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 378
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043188 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043188
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043188/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043188
Building REAL250005043189
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043189'
/scratch/stefan/7916125/working/building/REAL250005043189 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043189

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043189/0 /scratch/stefan/7916125/working/building/REAL250005043189 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/297
`/scratch/stefan/7916125/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)CO)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043189 none CC[C@@H]1[C@@H](NC(=O)CO)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 6, 22, 22, 66, 1, 1, 1, 1, 22] 123
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 11, 12, 13, 14, 34, 31] set([0, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 181
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043189 none CC[C@@H]1[C@@H](NC(=O)CO)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [28, 22, 22, 22, 22, 22, 22, 33, 33, 33, 36, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 33, 36, 36, 108, 22, 22, 22, 22, 1] 123
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 234
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043189 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043189
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043189/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043189
Building REAL250005043190
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043190'
/scratch/stefan/7916125/working/building/REAL250005043190 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043190

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043190/0 /scratch/stefan/7916125/working/building/REAL250005043190 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/298
`/scratch/stefan/7916125/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C(C)O)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043190 none CC[C@@H]1[C@@H](NC(=O)C(C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 6, 28, 28, 28, 28, 84, 1, 1, 1, 1, 23] 183
rigid atoms, others: [1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 34, 35, 36, 37] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 218
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043190 none CC[C@@H]1[C@@H](NC(=O)C(C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [29, 23, 23, 23, 23, 23, 23, 42, 42, 42, 61, 61, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 42, 61, 61, 61, 61, 183, 23, 23, 23, 23, 1] 183
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 415
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043190 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043190
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043190/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043190
Building REAL250005043191
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043191'
/scratch/stefan/7916125/working/building/REAL250005043191 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043191

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043191/0 /scratch/stefan/7916125/working/building/REAL250005043191 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/299
`/scratch/stefan/7916125/working/3D/299' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)CCF)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043191 none CC[C@@H]1[C@@H](NC(=O)CCF)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 36, 64, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 6, 36, 36, 64, 64, 1, 1, 1, 1, 21] 146
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 12, 13, 14, 15, 34, 35, 36] set([0, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37])
total number of confs: 300
number of broken/clashed sets: 99
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043191 none CC[C@@H]1[C@@H](NC(=O)CCF)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 5, 15, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [31, 21, 21, 21, 21, 21, 21, 55, 55, 55, 130, 138, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 55, 130, 130, 138, 138, 21, 21, 21, 21, 1] 146
rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 563
number of broken/clashed sets: 99
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043191 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043191
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043191/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043191
Building REAL250005043192
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043192'
/scratch/stefan/7916125/working/building/REAL250005043192 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043192

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043192/0 /scratch/stefan/7916125/working/building/REAL250005043192 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/300
`/scratch/stefan/7916125/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043192 none CC[C@@H]1[C@@H](NC(=O)[C@@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 6, 23, 23, 23, 69, 1, 1, 1, 1, 24] 165
rigid atoms, others: [1, 2, 3, 4, 5, 6, 13, 14, 15, 34, 35, 36, 16, 37] set([0, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 189
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043192 none CC[C@@H]1[C@@H](NC(=O)[C@@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 24, 24, 24, 24, 24, 24, 36, 36, 36, 52, 52, 52, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 36, 52, 52, 52, 156, 24, 24, 24, 24, 1] 165
rigid atoms, others: [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, 37])
total number of confs: 364
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043192 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043192
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043192/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043192
Building REAL250005043193
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043193'
/scratch/stefan/7916125/working/building/REAL250005043193 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043193

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043193/0 /scratch/stefan/7916125/working/building/REAL250005043193 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/301
`/scratch/stefan/7916125/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)[C@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043193 none CC[C@@H]1[C@@H](NC(=O)[C@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 6, 28, 28, 28, 84, 1, 1, 1, 1, 23] 183
rigid atoms, others: [1, 2, 3, 4, 5, 6, 13, 14, 15, 34, 35, 36, 16, 37] set([0, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38])
total number of confs: 218
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043193 none CC[C@@H]1[C@@H](NC(=O)[C@H](C)O)CCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [29, 23, 23, 23, 23, 23, 23, 42, 42, 42, 61, 61, 61, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 42, 61, 61, 61, 183, 23, 23, 23, 23, 1] 183
rigid atoms, others: [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, 37])
total number of confs: 415
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043193 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043193
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043193/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043193
Building REAL250005043194
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043194'
/scratch/stefan/7916125/working/building/REAL250005043194 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043194

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043194/0 /scratch/stefan/7916125/working/building/REAL250005043194 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/302
`/scratch/stefan/7916125/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC)

`REAL250005043194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043194 none CC=CC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 3, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 24, 3, 3, 3, 3, 3] 78
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 103
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043194 none CC=CC(=O)N[C@H]1CCN(C(=O)C2=CC(=O)[N-]O2)[C@@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 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, 3, 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
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 49, 49, 49, 24, 24, 24, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 24, 40, 73, 73, 73, 73, 73, 49, 24, 24, 24, 24, 1, 40, 40, 40, 40, 40] 78
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 303
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043194 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043194
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043194/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043194
Building REAL250005043195
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043195'
/scratch/stefan/7916125/working/building/REAL250005043195 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043195

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043195/0 /scratch/stefan/7916125/working/building/REAL250005043195 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/303
`/scratch/stefan/7916125/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)COC)

`REAL250005043195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043195 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)COC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 14, 22, 3, 3, 3, 3, 3, 6, 10, 1, 1, 1, 1, 14, 14, 22, 22, 22] 35
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 88
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043195 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)COC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
35  conformations in input
total number of sets (complete confs): 35
using default count positions algorithm for smaller data
unique positions, atoms: [14, 10, 10, 10, 4, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 15, 15, 29, 32, 14, 14, 14, 14, 14, 5, 1, 10, 10, 10, 10, 29, 29, 32, 32, 32] 35
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 142
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043195 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043195
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043195/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043195
Building REAL250005043196
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043196'
/scratch/stefan/7916125/working/building/REAL250005043196 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043196

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043196/0 /scratch/stefan/7916125/working/building/REAL250005043196 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/304
`/scratch/stefan/7916125/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC)

`REAL250005043196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043196 none CCCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [30, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 1, 1, 3, 32, 32, 32, 32, 32, 23, 23, 1, 1, 1, 1, 6, 17, 3, 3, 3, 3, 3] 77
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 19, 20, 21, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 174
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043196 none CCCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [62, 56, 28, 17, 28, 17, 17, 17, 7, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 24, 63, 63, 63, 63, 63, 56, 56, 17, 17, 17, 17, 8, 1, 24, 24, 24, 24, 24] 77
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 293
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043196 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043196
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043196/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043196
Building REAL250005043197
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043197'
/scratch/stefan/7916125/working/building/REAL250005043197 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043197

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043197/0 /scratch/stefan/7916125/working/building/REAL250005043197 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/305
`/scratch/stefan/7916125/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)C)

`REAL250005043197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043197 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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
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, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 10, 10, 3, 3, 3, 3, 3, 6, 9, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10] 22
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 64
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043197 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 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
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, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 19, 19, 21, 21, 11, 11, 11, 11, 11, 5, 1, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21] 22
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 77
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043197 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043197
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043197/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043197
Building REAL250005043198
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043198'
/scratch/stefan/7916125/working/building/REAL250005043198 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043198

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043198/0 /scratch/stefan/7916125/working/building/REAL250005043198 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/306
`/scratch/stefan/7916125/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC)

`REAL250005043198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043198 none CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 3, 12, 12, 12, 12, 12, 1, 1, 1, 1, 6, 14, 3, 3, 3, 3, 3] 33
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 70
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043198 none CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 21, 14, 21, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 21, 23, 23, 23, 23, 23, 14, 14, 14, 14, 7, 1, 21, 21, 21, 21, 21] 33
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 117
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043198 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043198
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043198/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043198
Building REAL250005043199
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043199'
/scratch/stefan/7916125/working/building/REAL250005043199 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043199

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043199/0 /scratch/stefan/7916125/working/building/REAL250005043199 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/307
`/scratch/stefan/7916125/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(C)=O)

`REAL250005043199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043199 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 3, 3, 3, 3, 3, 5, 8, 1, 1, 1, 1, 4, 4, 4] 15
rigid atoms, others: [1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 32, 34, 33, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 33
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043199 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 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: [10, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 11, 10, 10, 10, 10, 10, 5, 1, 8, 8, 8, 8, 11, 11, 11] 15
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 45
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043199 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043199
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043199/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043199
Building REAL250005043200
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043200'
/scratch/stefan/7916125/working/building/REAL250005043200 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043200

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043200/0 /scratch/stefan/7916125/working/building/REAL250005043200 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/308
`/scratch/stefan/7916125/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C1CC1)

`REAL250005043200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043200 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 12, 12, 3, 3, 3, 3, 3, 6, 10, 1, 1, 1, 1, 12, 12, 12, 12, 12] 31
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 58
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043200 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [12, 10, 10, 10, 6, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 29, 29, 12, 12, 12, 12, 12, 7, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29] 31
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 100
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: REAL250005043200 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [18, 12, 12, 12, 12, 12, 12, 26, 26, 26, 29, 29, 29, 29, 29, 12, 12, 7, 1, 7, 1, 1, 1, 18, 18, 18, 18, 18, 26, 29, 12, 12, 12, 12, 1, 1, 1, 1, 1] 31
rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 105
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043200 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043200
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043200/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043200
Building REAL250005043201
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043201'
/scratch/stefan/7916125/working/building/REAL250005043201 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043201

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043201/0 /scratch/stefan/7916125/working/building/REAL250005043201 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/309
`/scratch/stefan/7916125/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(N)=O)

`REAL250005043201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043201 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 6, 6, 16, 16, 3, 3, 3, 3, 3, 6, 14, 1, 1, 1, 1, 16, 16] 44
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 76
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043201 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
44  conformations in input
total number of sets (complete confs): 44
using default count positions algorithm for smaller data
unique positions, atoms: [19, 14, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 23, 36, 36, 19, 19, 19, 19, 19, 6, 1, 14, 14, 14, 14, 36, 36] 44
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 145
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043201 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043201
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043201/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043201
Building REAL250005043202
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043202'
/scratch/stefan/7916125/working/building/REAL250005043202 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043202

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043202/0 /scratch/stefan/7916125/working/building/REAL250005043202 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/310
`/scratch/stefan/7916125/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CO)

`REAL250005043202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043202 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 5, 5, 12, 3, 3, 3, 3, 3, 6, 14, 1, 1, 1, 1, 12, 12, 36] 114
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 107
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043202 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [22, 14, 14, 14, 6, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 20, 20, 25, 22, 22, 22, 22, 22, 7, 1, 14, 14, 14, 14, 25, 25, 75] 114
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 28] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 214
number of broken/clashed sets: 71
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043202 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043202
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043202/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043202
Building REAL250005043203
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043203'
/scratch/stefan/7916125/working/building/REAL250005043203 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043203

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043203/0 /scratch/stefan/7916125/working/building/REAL250005043203 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/311
`/scratch/stefan/7916125/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)O)

`REAL250005043203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043203 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 5, 5, 12, 12, 3, 3, 3, 3, 3, 6, 11, 1, 1, 1, 1, 12, 12, 12, 12, 36] 90
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38])
total number of confs: 107
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043203 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [15, 11, 11, 11, 5, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 16, 16, 25, 25, 15, 15, 15, 15, 15, 5, 1, 11, 11, 11, 11, 25, 25, 25, 25, 75] 90
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 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: 189
number of broken/clashed sets: 61
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043203 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043203
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043203/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043203
Building REAL250005043204
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043204'
/scratch/stefan/7916125/working/building/REAL250005043204 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043204

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043204/0 /scratch/stefan/7916125/working/building/REAL250005043204 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/312
`/scratch/stefan/7916125/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)=O)

`REAL250005043204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043204 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 14, 14, 3, 3, 3, 3, 3, 6, 9, 1, 1, 1, 1, 14, 14, 14] 31
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 62
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043204 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)C(C)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
31  conformations in input
total number of sets (complete confs): 31
using default count positions algorithm for smaller data
unique positions, atoms: [13, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 28, 28, 13, 13, 13, 13, 13, 4, 1, 9, 9, 9, 9, 28, 28, 28] 31
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 109
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043204 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043204
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043204/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043204
Building REAL250005043205
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043205'
/scratch/stefan/7916125/working/building/REAL250005043205 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043205

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043205/0 /scratch/stefan/7916125/working/building/REAL250005043205 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/313
`/scratch/stefan/7916125/working/3D/313' -> `0.mol2'
Preparing input files

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

`REAL250005043205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043205 none CC=CC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 3, 16, 16, 16, 16, 16, 1, 1, 1, 1, 6, 14, 3, 3, 3, 3, 3] 38
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 75
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043205 none CC=CC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 26, 14, 26, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 14, 14, 18, 35, 35, 35, 35, 35, 14, 14, 14, 14, 7, 1, 18, 18, 18, 18, 18] 38
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 127
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043205 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043205
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043205/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043205
Building REAL250005043206
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043206'
/scratch/stefan/7916125/working/building/REAL250005043206 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043206

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043206/0 /scratch/stefan/7916125/working/building/REAL250005043206 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/314
`/scratch/stefan/7916125/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@H](C)O)

`REAL250005043206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043206 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@H](C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 6, 14, 14, 14, 3, 3, 3, 3, 3, 6, 10, 1, 1, 1, 1, 14, 14, 14, 42] 84
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 15, 16, 17, 18, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 116
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043206 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@H](C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
84  conformations in input
total number of sets (complete confs): 84
using faster count positions algorithm for large data
unique positions, atoms: [13, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 27, 27, 27, 13, 13, 13, 13, 13, 6, 1, 10, 10, 10, 10, 27, 27, 27, 81] 84
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 193
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043206 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043206
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043206/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043206
Building REAL250005043207
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043207'
/scratch/stefan/7916125/working/building/REAL250005043207 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043207

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043207/0 /scratch/stefan/7916125/working/building/REAL250005043207 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/315
`/scratch/stefan/7916125/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC)

`REAL250005043207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043207 none C=CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [41, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 1, 1, 3, 41, 41, 41, 22, 22, 1, 1, 1, 1, 6, 16, 3, 3, 3, 3, 3] 78
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 165
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043207 none C=CCC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [68, 60, 34, 16, 34, 16, 16, 16, 5, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 16, 16, 23, 68, 68, 68, 60, 60, 16, 16, 16, 16, 5, 1, 23, 23, 23, 23, 23] 78
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 288
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043207 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043207
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043207/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043207
Building REAL250005043208
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043208'
/scratch/stefan/7916125/working/building/REAL250005043208 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043208

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043208/0 /scratch/stefan/7916125/working/building/REAL250005043208 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/316
`/scratch/stefan/7916125/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CC#N)

`REAL250005043208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043208 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 1, 5, 5, 25, 25, 3, 3, 3, 3, 3, 6, 11, 1, 1, 1, 1, 25, 25] 55
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 112
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043208 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [19, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 48, 48, 19, 19, 19, 19, 19, 5, 1, 11, 11, 11, 11, 48, 48] 55
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 229
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043208 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043208
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043208/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043208
Building REAL250005043209
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043209'
/scratch/stefan/7916125/working/building/REAL250005043209 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043209

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043209/0 /scratch/stefan/7916125/working/building/REAL250005043209 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/317
`/scratch/stefan/7916125/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CCF)

`REAL250005043209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043209 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 11, 20, 3, 3, 3, 3, 3, 6, 9, 1, 1, 1, 1, 11, 11, 20, 20] 40
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 15, 16, 17, 18, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 107
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043209 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 5, 15, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 9, 9, 3, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 35, 40, 11, 11, 11, 11, 11, 3, 1, 9, 9, 9, 9, 35, 35, 40, 40] 40
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 170
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043209 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043209
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043209/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043209
Building REAL250005043210
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043210'
/scratch/stefan/7916125/working/building/REAL250005043210 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043210

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043210/0 /scratch/stefan/7916125/working/building/REAL250005043210 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/318
`/scratch/stefan/7916125/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@@H](C)O)

`REAL250005043210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043210 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@@H](C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 10, 10, 10, 3, 3, 3, 3, 3, 6, 9, 1, 1, 1, 1, 10, 10, 10, 30] 57
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 15, 16, 17, 18, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 89
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043210 none CC[C@@H]1[C@@H](NC(=O)C2=CC(=O)[N-]O2)CCN1C(=O)[C@@H](C)O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 8, 1, 11, 5, 7, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [11, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 18, 18, 18, 11, 11, 11, 11, 11, 5, 1, 9, 9, 9, 9, 18, 18, 18, 54] 57
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 30] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 127
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043210 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043210
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043210/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043210
Building REAL250005043211
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043211'
/scratch/stefan/7916125/working/building/REAL250005043211 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043211

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043211/0 /scratch/stefan/7916125/working/building/REAL250005043211 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/319
`/scratch/stefan/7916125/working/3D/319' -> `0.mol2'
Preparing input files

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

`REAL250005043211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043211 none C=CC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 1, 1, 3, 12, 12, 12, 1, 1, 1, 1, 6, 15, 3, 3, 3, 3, 3] 30
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 18, 19, 20, 25, 26, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 66
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043211 none C=CC(=O)N1CC[C@H](NC(=O)C2=CC(=O)[N-]O2)[C@H]1CC NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 15, 20, 15, 15, 15, 7, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 22, 20, 20, 20, 15, 15, 15, 15, 7, 1, 22, 22, 22, 22, 22] 30
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 99
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043211 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043211
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043211/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043211
Building REAL250005043212
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043212'
/scratch/stefan/7916125/working/building/REAL250005043212 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043212

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043212/0 /scratch/stefan/7916125/working/building/REAL250005043212 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/320
`/scratch/stefan/7916125/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043212 none CC(=O)N1CCCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 13, 15, 5, 12, 12, 21, 21, 21, 21, 21, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 45, 21, 1, 1] 132
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 38, 20, 24, 25, 26, 27, 28, 29, 30, 37] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 31, 32, 33, 34, 35, 36])
total number of confs: 148
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043212 none CC(=O)N1CCCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 21, 35, 21, 21, 21, 21, 18, 8, 18, 28, 33, 1, 8, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 28, 28, 33, 33, 99, 1, 21, 21] 132
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 286
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043212 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043212
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043212/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043212
Building REAL250005043213
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043213'
/scratch/stefan/7916125/working/building/REAL250005043213 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043213

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043213/0 /scratch/stefan/7916125/working/building/REAL250005043213 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/321
`/scratch/stefan/7916125/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(CCO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043213 none CC(=O)N(CCO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 1, 3, 7, 13, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 7, 7, 7, 7, 7, 13, 13, 39, 1, 1, 1, 1, 1, 1, 1, 33, 1, 1] 270
rigid atoms, others: [32, 33, 34, 3, 37, 38, 7, 8, 9, 10, 11, 12, 35, 20, 29, 30, 31] set([0, 1, 2, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 36])
total number of confs: 155
number of broken/clashed sets: 213
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043213 none CC(=O)N(CCO)C1CCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [83, 47, 83, 33, 47, 72, 87, 33, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 83, 83, 83, 72, 72, 87, 87, 261, 33, 33, 33, 33, 33, 33, 33, 1, 33, 33] 270
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 720
number of broken/clashed sets: 213
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043213 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043213
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043213/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043213
Building REAL250005043214
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043214'
/scratch/stefan/7916125/working/building/REAL250005043214 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043214

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043214/0 /scratch/stefan/7916125/working/building/REAL250005043214 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/322
`/scratch/stefan/7916125/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1)

`REAL250005043214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043214 none CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 1, 25, 1, 1, 1, 1, 1, 1] 59
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38] set([0, 1, 3, 32, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27])
total number of confs: 80
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043214 none CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 54, 25, 54, 25, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 59, 59, 59, 59, 59, 25, 25, 25, 25, 1, 25, 25, 25, 25, 25, 25] 59
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043214 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043214
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043214/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043214
Building REAL250005043215
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043215'
/scratch/stefan/7916125/working/building/REAL250005043215 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043215

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043215/0 /scratch/stefan/7916125/working/building/REAL250005043215 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/323
`/scratch/stefan/7916125/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1)

`REAL250005043215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043215 none CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1] 21
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 29])
total number of confs: 41
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043215 none CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 15, 21, 15, 15, 15, 15, 15, 9, 1, 9, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 15, 1, 15, 15, 15, 15, 15, 15] 21
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35])
total number of confs: 54
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043215 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043215
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043215/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043215
Building REAL250005043216
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043216'
/scratch/stefan/7916125/working/building/REAL250005043216 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043216

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043216/0 /scratch/stefan/7916125/working/building/REAL250005043216 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/324
`/scratch/stefan/7916125/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1)

`REAL250005043216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043216 none O=C(CO)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 16, 16, 48, 1, 1, 1, 1, 33, 1, 1, 1, 1, 1, 1] 165
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 30])
total number of confs: 147
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043216 none O=C(CO)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)CC[C@@H]2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [46, 33, 46, 55, 33, 33, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 55, 55, 165, 33, 33, 33, 33, 1, 33, 33, 33, 33, 33, 33] 165
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 324
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043216 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043216
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043216/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043216
Building REAL250005043217
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043217'
/scratch/stefan/7916125/working/building/REAL250005043217 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043217

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043217/0 /scratch/stefan/7916125/working/building/REAL250005043217 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/325
`/scratch/stefan/7916125/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1)

`REAL250005043217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043217 none CCC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 20, 1, 1, 1, 1] 42
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38] set([0, 1, 34, 3, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043217 none CCC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 21, 42, 21, 21, 21, 21, 21, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 21, 21, 21, 42, 42, 42, 42, 42, 21, 21, 21, 21, 20, 20, 1, 20, 20, 21, 21] 42
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043217 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043217
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043217/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043217
Building REAL250005043218
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043218'
/scratch/stefan/7916125/working/building/REAL250005043218 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043218

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043218/0 /scratch/stefan/7916125/working/building/REAL250005043218 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/326
`/scratch/stefan/7916125/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1)

`REAL250005043218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043218 none CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 23, 1, 1, 1, 1] 33
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 31])
total number of confs: 46
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043218 none CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 24, 33, 24, 24, 23, 23, 24, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 33, 33, 33, 24, 24, 23, 24, 23, 23, 1, 23, 23, 24, 24] 33
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 82
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043218 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043218
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043218/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043218
Building REAL250005043219
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043219'
/scratch/stefan/7916125/working/building/REAL250005043219 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043219

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043219/0 /scratch/stefan/7916125/working/building/REAL250005043219 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/327
`/scratch/stefan/7916125/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1)

`REAL250005043219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043219 none O=C(CO)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 17, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 24, 1, 1, 1, 1, 17, 17, 51, 1, 1, 1, 1, 1, 1, 25, 1, 1, 1, 1] 144
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36] set([0, 32, 2, 3, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25])
total number of confs: 153
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043219 none O=C(CO)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [44, 25, 45, 48, 25, 25, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 25, 24, 48, 48, 144, 25, 25, 25, 25, 25, 25, 1, 24, 24, 25, 24] 144
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 274
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043219 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043219
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043219/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043219
Building REAL250005043220
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043220'
/scratch/stefan/7916125/working/building/REAL250005043220 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043220

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043220/0 /scratch/stefan/7916125/working/building/REAL250005043220 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/328
`/scratch/stefan/7916125/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1)

`REAL250005043220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043220 none C=CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 17, 17, 17, 1, 1, 1, 1, 1, 1, 22, 1, 1, 1, 1] 37
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36] set([0, 1, 3, 32, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043220 none C=CC(=O)N1CC[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@H]2C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 37, 23, 37, 23, 23, 23, 23, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 37, 37, 37, 23, 23, 23, 23, 22, 22, 1, 23, 23, 23, 23] 37
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 84
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043220 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043220
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043220/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043220
Building REAL250005043221
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043221'
/scratch/stefan/7916125/working/building/REAL250005043221 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043221

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043221/0 /scratch/stefan/7916125/working/building/REAL250005043221 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/329
`/scratch/stefan/7916125/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043221 none CCC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 168, 199, 102, 168, 102, 39, 19, 19, 15, 8, 15, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 168, 102, 102, 102, 102, 19, 19, 19, 19, 15, 15, 15, 1] 201
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 754
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043221 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043221
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043221/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043221
Building REAL250005043222
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043222'
/scratch/stefan/7916125/working/building/REAL250005043222 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043222

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043222/0 /scratch/stefan/7916125/working/building/REAL250005043222 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/330
`/scratch/stefan/7916125/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043222 none CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 90, 57, 29, 25, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 98, 98, 90, 90, 29, 29, 25, 25, 11, 11, 11, 1] 98
rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043222 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043222
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043222/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043222
Building REAL250005043223
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043223'
/scratch/stefan/7916125/working/building/REAL250005043223 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043223

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043223/0 /scratch/stefan/7916125/working/building/REAL250005043223 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/331
`/scratch/stefan/7916125/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043223 none CCC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 168, 199, 102, 168, 102, 39, 19, 19, 15, 8, 15, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 168, 102, 102, 102, 102, 19, 19, 19, 19, 15, 15, 15, 1] 201
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 754
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043223 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043223
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043223/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043223
Building REAL250005043224
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043224'
/scratch/stefan/7916125/working/building/REAL250005043224 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043224

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043224/0 /scratch/stefan/7916125/working/building/REAL250005043224 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/332
`/scratch/stefan/7916125/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043224 none CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 98, 98, 90, 57, 29, 25, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 98, 98, 98, 98, 98, 98, 98, 98, 90, 90, 29, 29, 25, 25, 11, 11, 11, 1] 98
rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 365
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043224 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043224
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043224/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043224
Building REAL250005043225
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043225'
/scratch/stefan/7916125/working/building/REAL250005043225 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043225

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043225/0 /scratch/stefan/7916125/working/building/REAL250005043225 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/333
`/scratch/stefan/7916125/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043225 none C=CC(=O)N(C)CCOCCN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 169, 201, 96, 169, 96, 43, 21, 21, 17, 8, 17, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 169, 169, 169, 96, 96, 96, 96, 21, 21, 21, 21, 17, 17, 17, 1] 201
rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 724
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043225 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043225
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043225/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043225
Building REAL250005043226
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043226'
/scratch/stefan/7916125/working/building/REAL250005043226 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043226

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043226/0 /scratch/stefan/7916125/working/building/REAL250005043226 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/334
`/scratch/stefan/7916125/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043226 none CCC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 1, 1] 15
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40] set([0, 1, 3, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25])
total number of confs: 42
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043226 none CCC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 15, 10, 10, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 10, 10] 15
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 39
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043226 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043226
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043226/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043226
Building REAL250005043227
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043227'
/scratch/stefan/7916125/working/building/REAL250005043227 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043227

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043227/0 /scratch/stefan/7916125/working/building/REAL250005043227 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/335
`/scratch/stefan/7916125/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043227 none CC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 1, 1] 16
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37] set([0, 2, 34, 11, 12, 13, 14, 15, 16, 17, 18, 35, 20, 21, 22])
total number of confs: 33
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043227 none CC(=O)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 16, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 10, 10] 16
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 49
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043227 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043227
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043227/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043227
Building REAL250005043228
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043228'
/scratch/stefan/7916125/working/building/REAL250005043228 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043228

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043228/0 /scratch/stefan/7916125/working/building/REAL250005043228 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/336
`/scratch/stefan/7916125/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043228 none O=C(CO)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 1, 1] 69
rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38] set([0, 35, 2, 3, 36, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23])
total number of confs: 94
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043228 none O=C(CO)N1CCCCCC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [20, 15, 20, 23, 15, 15, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 23, 23, 69, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 15, 15] 69
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 146
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043228 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043228
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043228/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043228
Building REAL250005043229
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043229'
/scratch/stefan/7916125/working/building/REAL250005043229 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043229

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043229/0 /scratch/stefan/7916125/working/building/REAL250005043229 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/337
`/scratch/stefan/7916125/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043229 none CCC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 29, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 1, 1] 59
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40] set([0, 1, 2, 3, 38, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 130
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043229 none CCC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [59, 40, 40, 40, 22, 22, 22, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 22, 59, 59, 59, 59, 59, 40, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 22, 22] 59
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 209
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043229 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043229
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043229/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043229
Building REAL250005043230
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043230'
/scratch/stefan/7916125/working/building/REAL250005043230 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043230

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043230/0 /scratch/stefan/7916125/working/building/REAL250005043230 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/338
`/scratch/stefan/7916125/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043230 none CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1] 23
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37] set([0, 1, 2, 35, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23])
total number of confs: 41
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043230 none CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 23, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17] 23
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 56
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043230 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043230
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043230/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043230
Building REAL250005043231
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043231'
/scratch/stefan/7916125/working/building/REAL250005043231 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043231

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043231/0 /scratch/stefan/7916125/working/building/REAL250005043231 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/339
`/scratch/stefan/7916125/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043231 none O=C(CO)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 28, 28, 84, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 1, 1] 153
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 209
number of broken/clashed sets: 153
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043231 none O=C(CO)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
153  conformations in input
total number of sets (complete confs): 153
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 51, 21, 21, 21, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 51, 51, 153, 44, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21] 153
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 306
number of broken/clashed sets: 153
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043231 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043231
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043231/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043231
Building REAL250005043232
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043232'
/scratch/stefan/7916125/working/building/REAL250005043232 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043232

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043232/0 /scratch/stefan/7916125/working/building/REAL250005043232 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/340
`/scratch/stefan/7916125/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043232 none C=CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 1, 1] 39
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 75
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043232 none C=CC(=O)NC1CCCCCN(C(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 39, 39, 39, 19, 19, 19, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 19, 19] 39
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 99
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043232 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043232
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043232/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043232
Building REAL250005043233
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043233'
/scratch/stefan/7916125/working/building/REAL250005043233 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043233

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043233/0 /scratch/stefan/7916125/working/building/REAL250005043233 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/341
`/scratch/stefan/7916125/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043233 none CCC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 38, 38, 63, 63, 63, 63, 63, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 63] 75
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 27, 28, 29, 30, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40])
total number of confs: 180
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043233 none CCC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 69, 63, 69, 63, 63, 63, 63, 63, 46, 63, 31, 11, 31, 1, 11, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 63, 63, 63, 63, 63, 63, 63, 63, 46, 46, 31, 31, 31, 1] 75
rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 275
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043233 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043233
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043233/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043233
Building REAL250005043234
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043234'
/scratch/stefan/7916125/working/building/REAL250005043234 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043234

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043234/0 /scratch/stefan/7916125/working/building/REAL250005043234 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/342
`/scratch/stefan/7916125/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043234 none CC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 13] 13
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 34, 36, 37, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23])
total number of confs: 49
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043234 none CC(=O)N1CCCC[C@H]1CN(C)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 12, 13, 11, 6, 11, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 11, 11, 11, 1] 13
rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 39
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043234 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043234
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043234/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043234
Building REAL250005043235
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043235'
/scratch/stefan/7916125/working/building/REAL250005043235 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043235

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043235/0 /scratch/stefan/7916125/working/building/REAL250005043235 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/343
`/scratch/stefan/7916125/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C[C@@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1)

`REAL250005043235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043235 none CN(C[C@@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 8, 12, 12, 16, 16, 16, 16, 16, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 16] 66
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38])
total number of confs: 93
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043235 none CN(C[C@@H]1CCCCN1C(=O)CO)C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 10, 13, 16, 16, 16, 16, 16, 16, 16, 18, 18, 22, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 66, 1] 66
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 150
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043235 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043235
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043235/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043235
Building REAL250005043236
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043236'
/scratch/stefan/7916125/working/building/REAL250005043236 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043236

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043236/0 /scratch/stefan/7916125/working/building/REAL250005043236 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/344
`/scratch/stefan/7916125/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043236 none CCC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 26, 11, 26, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12] 48
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 39, 38] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40])
total number of confs: 122
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043236 none CCC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [48, 47, 33, 47, 18, 33, 12, 12, 12, 12, 12, 12, 12, 9, 1, 9, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 33, 33, 33, 18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 1] 48
rigid atoms, others: [40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 163
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043236 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043236
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043236/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043236
Building REAL250005043237
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043237'
/scratch/stefan/7916125/working/building/REAL250005043237 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043237

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043237/0 /scratch/stefan/7916125/working/building/REAL250005043237 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/345
`/scratch/stefan/7916125/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043237 none CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [16, 10, 16, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 16, 16, 16, 10, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15] 37
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 77
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043237 none CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 31, 37, 22, 31, 15, 15, 15, 15, 15, 15, 15, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 31, 31, 31, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 1] 37
rigid atoms, others: [37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 129
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043237 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043237
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043237/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043237
Building REAL250005043238
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043238'
/scratch/stefan/7916125/working/building/REAL250005043238 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043238

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043238/0 /scratch/stefan/7916125/working/building/REAL250005043238 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/346
`/scratch/stefan/7916125/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO)

`REAL250005043238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043238 none CN(C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.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, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 12, 21, 21, 34, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 34, 34, 102] 138
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38])
total number of confs: 261
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043238 none CN(C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'O.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, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [35, 22, 16, 16, 16, 16, 16, 16, 16, 11, 1, 11, 1, 1, 1, 1, 1, 1, 35, 45, 45, 46, 35, 35, 35, 22, 22, 16, 16, 16, 16, 16, 16, 16, 16, 1, 46, 46, 138] 138
rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38])
total number of confs: 293
number of broken/clashed sets: 31
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043238 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043238
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043238/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043238
Building REAL250005043239
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043239'
/scratch/stefan/7916125/working/building/REAL250005043239 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043239

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043239/0 /scratch/stefan/7916125/working/building/REAL250005043239 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/347
`/scratch/stefan/7916125/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043239 none C=CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 23, 11, 23, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 16, 16, 16, 32, 32, 32, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16] 48
rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38])
total number of confs: 124
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043239 none C=CC(=O)N(C)C[C@@H]1CCCCN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 35, 48, 22, 35, 16, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 1, 1, 1, 48, 48, 48, 35, 35, 35, 22, 22, 16, 16, 16, 16, 16, 16, 16, 16, 1] 48
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 155
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043239 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043239
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043239/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043239
Building REAL250005043240
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043240'
/scratch/stefan/7916125/working/building/REAL250005043240 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043240

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043240/0 /scratch/stefan/7916125/working/building/REAL250005043240 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/348
`/scratch/stefan/7916125/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1)

`REAL250005043240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043240 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 28, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 29
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 39, 16, 17, 18, 19, 20, 40, 25, 26, 27, 28, 29, 31] set([0, 1, 2, 34, 36, 37, 38, 33, 9, 10, 11, 12, 13, 14, 15, 35, 21, 22, 23, 24, 30])
total number of confs: 64
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043240 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 28, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 29, 29, 29, 29, 28, 28, 28, 28, 28, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 29
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 52
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043240 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043240
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043240/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043240
Building REAL250005043241
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043241'
/scratch/stefan/7916125/working/building/REAL250005043241 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043241

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043241/0 /scratch/stefan/7916125/working/building/REAL250005043241 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/349
`/scratch/stefan/7916125/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1)

`REAL250005043241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043241 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 4, 7, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 10
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 40, 39, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31] set([0, 33, 2, 34, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 35, 21, 22, 23, 29, 30])
total number of confs: 38
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043241 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)CC(C)(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
10  conformations in input
total number of sets (complete confs): 10
using default count positions algorithm for smaller data
unique positions, atoms: [10, 7, 10, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 10, 7, 7, 7, 7, 7, 4, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 10
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 31
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043241 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043241
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043241/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043241
Building REAL250005043242
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043242'
/scratch/stefan/7916125/working/building/REAL250005043242 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043242

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043242/0 /scratch/stefan/7916125/working/building/REAL250005043242 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/350
`/scratch/stefan/7916125/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043242 none CC(=O)N1CCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
345  conformations in input
total number of sets (complete confs): 345
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 7, 21, 25, 7, 19, 19, 51, 51, 51, 51, 51, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 21, 21, 25, 25, 75, 51, 1, 1, 1, 1] 345
rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 36, 19, 20, 24, 25, 26, 27, 28, 37, 35] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34])
total number of confs: 260
number of broken/clashed sets: 186
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043242 none CC(=O)N1CCC(N(CCO)C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 12, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
345  conformations in input
total number of sets (complete confs): 345
using faster count positions algorithm for large data
unique positions, atoms: [91, 51, 91, 51, 51, 51, 33, 10, 33, 65, 75, 1, 10, 1, 1, 1, 1, 1, 1, 51, 51, 91, 91, 91, 51, 51, 51, 51, 51, 65, 65, 75, 75, 225, 1, 51, 51, 51, 51] 345
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 718
number of broken/clashed sets: 186
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043242 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043242
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043242/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043242
Building REAL250005043243
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043243'
/scratch/stefan/7916125/working/building/REAL250005043243 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043243

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043243/0 /scratch/stefan/7916125/working/building/REAL250005043243 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/351
`/scratch/stefan/7916125/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(CCO)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043243 none CC(=O)N(CCO)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
384  conformations in input
total number of sets (complete confs): 384
using faster count positions algorithm for large data
unique positions, atoms: [12, 5, 12, 1, 5, 10, 17, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 12, 12, 12, 10, 10, 17, 17, 51, 1, 1, 1, 1, 1, 32, 1, 1, 1, 1] 384
rigid atoms, others: [32, 33, 3, 36, 37, 35, 7, 8, 9, 10, 11, 19, 20, 38, 29, 30, 31] set([0, 1, 2, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 34])
total number of confs: 186
number of broken/clashed sets: 238
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043243 none CC(=O)N(CCO)C1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
384  conformations in input
total number of sets (complete confs): 384
using faster count positions algorithm for large data
unique positions, atoms: [126, 45, 126, 32, 45, 84, 128, 32, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 32, 126, 126, 126, 84, 84, 128, 128, 384, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32] 384
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1174
number of broken/clashed sets: 238
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043243 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043243
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043243/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043243
Building REAL250005043244
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043244'
/scratch/stefan/7916125/working/building/REAL250005043244 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043244

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043244/0 /scratch/stefan/7916125/working/building/REAL250005043244 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/352
`/scratch/stefan/7916125/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC1CCC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1)

`REAL250005043244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043244 none CC(=O)NCC1CCC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 20, 20, 20, 20, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 15] 34
rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 38, 39, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 40])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043244 none CC(=O)NCC1CCC(C)(C)CN1C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 28, 15, 15, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 28, 28, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 34
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 115
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043244 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043244
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043244/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043244
Building REAL250005043245
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043245'
/scratch/stefan/7916125/working/building/REAL250005043245 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043245

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043245/0 /scratch/stefan/7916125/working/building/REAL250005043245 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/353
`/scratch/stefan/7916125/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC(C)(C)CCC1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043245 none CC(=O)N1CC(C)(C)CCC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 15, 15, 15, 15, 15, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 14, 15] 15
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 24, 25, 33, 36] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40])
total number of confs: 62
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043245 none CC(=O)N1CC(C)(C)CCC1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 5, 1] 15
rigid atoms, others: [40, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 54
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043245 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043245
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043245/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043245
Building REAL250005043246
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043246'
/scratch/stefan/7916125/working/building/REAL250005043246 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043246

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043246/0 /scratch/stefan/7916125/working/building/REAL250005043246 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/354
`/scratch/stefan/7916125/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043246 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 29, 1, 1, 1, 3] 183
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 17, 18, 19, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 35, 20, 21, 22, 23, 24, 25, 31])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043246 none CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [61, 44, 44, 44, 29, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 29, 61, 61, 61, 61, 61, 44, 29, 29, 29, 29, 29, 1, 29, 29, 29, 87] 183
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 289
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043246 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043246
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043246/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043246
Building REAL250005043247
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043247'
/scratch/stefan/7916125/working/building/REAL250005043247 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043247

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043247/0 /scratch/stefan/7916125/working/building/REAL250005043247 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/355
`/scratch/stefan/7916125/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043247 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 20, 1, 1, 1, 3] 63
rigid atoms, others: [3, 4, 5, 6, 7, 8, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 32, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 28])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043247 none CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [21, 21, 21, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 21, 21, 21, 21, 20, 20, 20, 20, 20, 1, 20, 20, 20, 60] 63
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 101
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043247 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043247
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043247/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043247
Building REAL250005043248
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043248'
/scratch/stefan/7916125/working/building/REAL250005043248 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043248

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043248/0 /scratch/stefan/7916125/working/building/REAL250005043248 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/356
`/scratch/stefan/7916125/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)C1CC1)

`REAL250005043248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043248 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 1, 5, 24, 24, 5, 1, 1, 1, 1, 1, 30, 1, 1, 1, 6, 24, 24, 24, 24, 24] 231
rigid atoms, others: [2, 3, 4, 5, 6, 7, 15, 16, 17, 22, 23, 24, 25, 26, 28, 29, 30] set([0, 1, 34, 35, 36, 33, 32, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 27, 31])
total number of confs: 106
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043248 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 30, 52, 78, 78, 52, 30, 30, 30, 30, 30, 1, 30, 30, 30, 90, 78, 78, 78, 78, 78] 234
rigid atoms, others: [7, 9, 10, 11, 12, 13, 14, 27] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 308
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043248 none O=C(NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 24, 24, 24, 24, 66, 66, 78, 78, 78, 78, 78, 24, 24, 24, 1, 1, 1, 10, 24, 24, 24, 24, 24, 78, 24, 24, 24, 72, 1, 1, 1, 1, 1] 234
rigid atoms, others: [32, 1, 34, 35, 36, 33, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 271
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043248 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043248
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043248/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043248
Building REAL250005043249
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043249'
/scratch/stefan/7916125/working/building/REAL250005043249 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043249

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043249/0 /scratch/stefan/7916125/working/building/REAL250005043249 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/357
`/scratch/stefan/7916125/working/3D/357' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043249 none COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
276  conformations in input
total number of sets (complete confs): 276
using faster count positions algorithm for large data
unique positions, atoms: [38, 30, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 38, 38, 38, 30, 30, 6, 1, 1, 1, 1, 1, 31, 1, 1, 1, 3] 276
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043249 none COCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
276  conformations in input
total number of sets (complete confs): 276
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 57, 57, 57, 31, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 31, 92, 92, 92, 92, 92, 57, 31, 31, 31, 31, 31, 1, 31, 31, 31, 93] 276
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 415
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043249 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043249
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043249/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043249
Building REAL250005043250
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043250'
/scratch/stefan/7916125/working/building/REAL250005043250 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043250

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043250/0 /scratch/stefan/7916125/working/building/REAL250005043250 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/358
`/scratch/stefan/7916125/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043250 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 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
435  conformations in input
total number of sets (complete confs): 435
using faster count positions algorithm for large data
unique positions, atoms: [47, 37, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 1, 55, 55, 55, 55, 55, 37, 37, 6, 1, 1, 1, 1, 1, 34, 1, 1, 1, 3] 435
rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 38])
total number of confs: 322
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043250 none CCCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 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
435  conformations in input
total number of sets (complete confs): 435
using faster count positions algorithm for large data
unique positions, atoms: [145, 138, 72, 72, 72, 34, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 145, 145, 145, 145, 145, 138, 138, 72, 34, 34, 34, 34, 34, 1, 34, 34, 34, 102] 435
rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 619
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043250 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043250
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043250/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043250
Building REAL250005043251
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043251'
/scratch/stefan/7916125/working/building/REAL250005043251 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043251

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043251/0 /scratch/stefan/7916125/working/building/REAL250005043251 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/359
`/scratch/stefan/7916125/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043251 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 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
219  conformations in input
total number of sets (complete confs): 219
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 37, 1, 1, 1, 3] 219
rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 38])
total number of confs: 135
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043251 none CC(C)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 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
219  conformations in input
total number of sets (complete confs): 219
using faster count positions algorithm for large data
unique positions, atoms: [73, 62, 73, 62, 62, 37, 37, 37, 37, 11, 1, 11, 1, 1, 1, 1, 1, 1, 37, 37, 37, 73, 73, 73, 73, 73, 73, 73, 62, 37, 37, 37, 37, 37, 1, 37, 37, 37, 111] 219
rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 313
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043251 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043251
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043251/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043251
Building REAL250005043252
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043252'
/scratch/stefan/7916125/working/building/REAL250005043252 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043252

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043252/0 /scratch/stefan/7916125/working/building/REAL250005043252 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/360
`/scratch/stefan/7916125/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043252 none NC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 18, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 18, 18, 6, 1, 1, 1, 1, 1, 20, 1, 1, 1, 3] 150
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 33, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 29])
total number of confs: 79
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043252 none NC(=O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
150  conformations in input
total number of sets (complete confs): 150
using faster count positions algorithm for large data
unique positions, atoms: [50, 39, 50, 39, 39, 20, 20, 20, 20, 11, 1, 11, 1, 1, 1, 1, 1, 1, 20, 20, 20, 50, 50, 39, 20, 20, 20, 20, 20, 1, 20, 20, 20, 60] 150
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 196
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043252 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043252
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043252/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043252
Building REAL250005043253
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043253'
/scratch/stefan/7916125/working/building/REAL250005043253 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043253

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043253/0 /scratch/stefan/7916125/working/building/REAL250005043253 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/361
`/scratch/stefan/7916125/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043253 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
285  conformations in input
total number of sets (complete confs): 285
using faster count positions algorithm for large data
unique positions, atoms: [43, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 43, 43, 43, 29, 29, 6, 1, 1, 1, 1, 1, 29, 1, 1, 1, 3] 285
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043253 none C=CCC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
285  conformations in input
total number of sets (complete confs): 285
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 46, 46, 46, 29, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 29, 95, 95, 95, 95, 95, 46, 29, 29, 29, 29, 29, 1, 29, 29, 29, 87] 285
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 421
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043253 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043253
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043253/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043253
Building REAL250005043254
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043254'
/scratch/stefan/7916125/working/building/REAL250005043254 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043254

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043254/0 /scratch/stefan/7916125/working/building/REAL250005043254 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/362
`/scratch/stefan/7916125/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043254 none O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
360  conformations in input
total number of sets (complete confs): 360
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 20, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 1, 20, 20, 60, 6, 1, 1, 1, 1, 1, 21, 1, 1, 1, 3] 360
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 29])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043254 none O=C(CO)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
360  conformations in input
total number of sets (complete confs): 360
using faster count positions algorithm for large data
unique positions, atoms: [35, 35, 35, 40, 21, 21, 21, 21, 10, 1, 10, 1, 1, 1, 1, 1, 1, 21, 21, 21, 40, 40, 120, 35, 21, 21, 21, 21, 21, 1, 21, 21, 21, 63] 360
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 298
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043254 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043254
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043254/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043254
Building REAL250005043255
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043255'
/scratch/stefan/7916125/working/building/REAL250005043255 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043255

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043255/0 /scratch/stefan/7916125/working/building/REAL250005043255 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/363
`/scratch/stefan/7916125/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043255 none CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
576  conformations in input
total number of sets (complete confs): 576
using faster count positions algorithm for large data
unique positions, atoms: [25, 6, 24, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 1, 25, 25, 25, 25, 75, 6, 1, 1, 1, 1, 1, 27, 1, 1, 1, 3] 576
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 202
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043255 none CC(O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
576  conformations in input
total number of sets (complete confs): 576
using faster count positions algorithm for large data
unique positions, atoms: [64, 47, 63, 47, 47, 27, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 27, 64, 64, 64, 64, 192, 47, 27, 27, 27, 27, 27, 1, 27, 27, 27, 81] 576
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 465
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043255 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043255
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043255/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043255
Building REAL250005043256
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043256'
/scratch/stefan/7916125/working/building/REAL250005043256 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043256

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043256/0 /scratch/stefan/7916125/working/building/REAL250005043256 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/364
`/scratch/stefan/7916125/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043256 none C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
504  conformations in input
total number of sets (complete confs): 504
using faster count positions algorithm for large data
unique positions, atoms: [21, 6, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 21, 21, 21, 63, 6, 1, 1, 1, 1, 1, 26, 1, 1, 1, 3] 504
rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 36])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043256 none C[C@@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
504  conformations in input
total number of sets (complete confs): 504
using faster count positions algorithm for large data
unique positions, atoms: [56, 39, 56, 56, 39, 39, 26, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 56, 56, 56, 168, 39, 26, 26, 26, 26, 26, 1, 26, 26, 26, 78] 504
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043256 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043256
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043256/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043256
Building REAL250005043257
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043257'
/scratch/stefan/7916125/working/building/REAL250005043257 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043257

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043257/0 /scratch/stefan/7916125/working/building/REAL250005043257 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/365
`/scratch/stefan/7916125/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043257 none C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
504  conformations in input
total number of sets (complete confs): 504
using faster count positions algorithm for large data
unique positions, atoms: [21, 6, 21, 21, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 21, 21, 21, 63, 6, 1, 1, 1, 1, 1, 26, 1, 1, 1, 6] 504
rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 36])
total number of confs: 178
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043257 none C[C@H](O)C(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
504  conformations in input
total number of sets (complete confs): 504
using faster count positions algorithm for large data
unique positions, atoms: [56, 39, 56, 56, 39, 39, 26, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 26, 56, 56, 56, 168, 39, 26, 26, 26, 26, 26, 1, 26, 26, 26, 78] 504
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043257 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043257
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043257/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043257
Building REAL250005043258
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043258'
/scratch/stefan/7916125/working/building/REAL250005043258 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043258

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043258/0 /scratch/stefan/7916125/working/building/REAL250005043258 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/366
`/scratch/stefan/7916125/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O)

`REAL250005043258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043258 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [21, 21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 1, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 23, 1, 1, 1, 3] 144
rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 32, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 36])
total number of confs: 91
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043258 none CC=CC(=O)NC1CCN(C(=O)C2=CC(=O)[N-]O2)CC1O NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 35, 35, 35, 23, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 23, 48, 48, 48, 48, 48, 35, 23, 23, 23, 23, 23, 1, 23, 23, 23, 69] 144
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 202
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043258 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043258
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043258/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043258
Building REAL250005043259
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043259'
/scratch/stefan/7916125/working/building/REAL250005043259 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043259

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043259/0 /scratch/stefan/7916125/working/building/REAL250005043259 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/367
`/scratch/stefan/7916125/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043259 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [40, 21, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 40, 40, 40, 21, 21, 1, 1, 1, 1, 1, 5, 11, 1, 3, 1, 1] 156
rigid atoms, others: [33, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 34, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31])
total number of confs: 130
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043259 none COCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [52, 48, 30, 11, 30, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 52, 52, 52, 48, 48, 11, 11, 11, 11, 11, 5, 1, 11, 33, 11, 11] 156
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 217
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043259 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043259
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043259/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043259
Building REAL250005043260
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043260'
/scratch/stefan/7916125/working/building/REAL250005043260 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043260

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043260/0 /scratch/stefan/7916125/working/building/REAL250005043260 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/368
`/scratch/stefan/7916125/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043260 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [28, 18, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 29, 29, 29, 28, 28, 18, 18, 1, 1, 1, 1, 1, 5, 12, 1, 3, 1, 1] 144
rigid atoms, others: [32, 35, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 37, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 33, 34, 36])
total number of confs: 157
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043260 none CCCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 31, 12, 31, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12, 6, 1, 12, 36, 12, 12] 144
rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 211
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043260 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043260
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043260/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043260
Building REAL250005043261
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043261'
/scratch/stefan/7916125/working/building/REAL250005043261 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043261

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043261/0 /scratch/stefan/7916125/working/building/REAL250005043261 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/369
`/scratch/stefan/7916125/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043261 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 1, 7, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 7, 1, 3, 1, 1] 66
rigid atoms, others: [32, 35, 3, 5, 6, 7, 8, 9, 38, 18, 19, 20, 37, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 33, 34, 36])
total number of confs: 55
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043261 none CC(C)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 7, 22, 7, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 5, 1, 7, 21, 7, 7] 66
rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 78
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043261 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043261
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043261/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043261
Building REAL250005043262
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043262'
/scratch/stefan/7916125/working/building/REAL250005043262 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043262

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043262/0 /scratch/stefan/7916125/working/building/REAL250005043262 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/370
`/scratch/stefan/7916125/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043262 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [11, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 12, 12, 12, 11, 11, 1, 1, 1, 1, 1, 6, 11, 1, 6, 1, 1] 72
rigid atoms, others: [32, 2, 35, 4, 5, 6, 7, 8, 34, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 1, 3, 33, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 30, 31])
total number of confs: 74
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043262 none CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 11, 24, 11, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 7, 1, 11, 33, 11, 11] 72
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 96
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043262 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043262
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043262/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043262
Building REAL250005043263
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043263'
/scratch/stefan/7916125/working/building/REAL250005043263 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043263

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043263/0 /scratch/stefan/7916125/working/building/REAL250005043263 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/371
`/scratch/stefan/7916125/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043263 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 5, 8, 1, 3, 1, 1] 39
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 16, 17, 18, 22, 23, 24, 25, 26, 29, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 27, 28, 30])
total number of confs: 28
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043263 none CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [13, 8, 13, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 8, 8, 8, 8, 5, 1, 8, 24, 8, 8] 39
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 63
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043263 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043263
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043263/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043263
Building REAL250005043264
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043264'
/scratch/stefan/7916125/working/building/REAL250005043264 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043264

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043264/0 /scratch/stefan/7916125/working/building/REAL250005043264 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/372
`/scratch/stefan/7916125/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CCN(C(=O)C2CC2)CC1O)C1=CC(=O)[N-]O1)

`REAL250005043264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043264 none O=C(NC1CCN(C(=O)C2CC2)CC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 1, 1, 1, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 1, 3, 9] 87
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 12, 13, 14, 34, 22, 23, 24, 25, 26] set([0, 1, 35, 36, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31])
total number of confs: 54
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043264 none O=C(NC1CCN(C(=O)C2CC2)CC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 12, 12, 12, 25, 29, 29, 29, 29, 29, 25, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 36, 29] 87
rigid atoms, others: [7, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36])
total number of confs: 113
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: REAL250005043264 none O=C(NC1CCN(C(=O)C2CC2)CC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 18, 18, 29, 29, 9, 9, 9, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 9, 9, 9, 27, 1] 87
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 124
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043264 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043264
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043264/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043264
Building REAL250005043265
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043265'
/scratch/stefan/7916125/working/building/REAL250005043265 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043265

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043265/0 /scratch/stefan/7916125/working/building/REAL250005043265 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/373
`/scratch/stefan/7916125/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043265 none NC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 1, 1, 19, 19, 1, 1, 1, 1, 1, 6, 11, 1, 3, 1, 1] 102
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 25, 26, 27, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29, 31])
total number of confs: 74
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043265 none NC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [34, 26, 34, 11, 26, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 34, 34, 11, 11, 11, 11, 11, 6, 1, 11, 33, 11, 11] 102
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 136
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043265 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043265
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043265/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043265
Building REAL250005043266
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043266'
/scratch/stefan/7916125/working/building/REAL250005043266 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043266

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043266/0 /scratch/stefan/7916125/working/building/REAL250005043266 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/374
`/scratch/stefan/7916125/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043266 none O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 14, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 1, 1, 14, 14, 42, 1, 1, 1, 1, 1, 5, 15, 1, 3, 1, 1] 234
rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 17, 18, 19, 23, 24, 25, 26, 27, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29, 31])
total number of confs: 121
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043266 none O=C(CO)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [26, 15, 26, 26, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 15, 15, 26, 26, 78, 15, 15, 15, 15, 15, 7, 1, 15, 45, 15, 15] 234
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 194
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043266 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043266
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043266/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043266
Building REAL250005043267
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043267'
/scratch/stefan/7916125/working/building/REAL250005043267 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043267

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043267/0 /scratch/stefan/7916125/working/building/REAL250005043267 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/375
`/scratch/stefan/7916125/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043267 none CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 14, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 1, 1, 14, 14, 14, 14, 42, 1, 1, 1, 1, 1, 5, 8, 1, 3, 1, 1] 252
rigid atoms, others: [33, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 34, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31])
total number of confs: 115
number of broken/clashed sets: 111
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043267 none CC(O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
252  conformations in input
total number of sets (complete confs): 252
using faster count positions algorithm for large data
unique positions, atoms: [28, 24, 28, 8, 24, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 28, 28, 28, 84, 8, 8, 8, 8, 8, 5, 1, 8, 24, 8, 8] 252
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 197
number of broken/clashed sets: 111
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043267 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043267
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043267/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043267
Building REAL250005043268
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043268'
/scratch/stefan/7916125/working/building/REAL250005043268 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043268

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043268/0 /scratch/stefan/7916125/working/building/REAL250005043268 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/376
`/scratch/stefan/7916125/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043268 none CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 22, 22, 22, 1, 1, 1, 1, 1, 6, 13, 1, 3, 1, 1] 99
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 18, 19, 20, 24, 25, 26, 27, 28, 31] set([0, 1, 2, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 29, 30])
total number of confs: 84
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043268 none CC(=O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [33, 26, 33, 13, 26, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 33, 33, 33, 13, 13, 13, 13, 13, 7, 1, 13, 39, 13, 13] 99
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 142
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043268 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043268
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043268/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043268
Building REAL250005043269
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043269'
/scratch/stefan/7916125/working/building/REAL250005043269 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043269

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043269/0 /scratch/stefan/7916125/working/building/REAL250005043269 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/377
`/scratch/stefan/7916125/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043269 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 1, 1, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 6, 18, 1, 4, 1, 1] 117
rigid atoms, others: [33, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 34, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31])
total number of confs: 85
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043269 none CC=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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: [5, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 36, 18, 36, 18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 18, 18, 39, 39, 39, 39, 39, 18, 18, 18, 18, 18, 10, 1, 18, 54, 18, 18] 117
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 169
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043269 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043269
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043269/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043269
Building REAL250005043270
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043270'
/scratch/stefan/7916125/working/building/REAL250005043270 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043270

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043270/0 /scratch/stefan/7916125/working/building/REAL250005043270 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/378
`/scratch/stefan/7916125/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043270 none C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 15, 15, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 15, 15, 15, 45, 1, 1, 1, 1, 1, 5, 10, 1, 3, 1, 1] 198
rigid atoms, others: [33, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 34, 31])
total number of confs: 123
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043270 none C[C@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [22, 21, 22, 22, 10, 21, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 22, 66, 10, 10, 10, 10, 10, 7, 1, 10, 30, 10, 10] 198
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 157
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043270 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043270
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043270/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043270
Building REAL250005043271
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043271'
/scratch/stefan/7916125/working/building/REAL250005043271 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043271

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043271/0 /scratch/stefan/7916125/working/building/REAL250005043271 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/379
`/scratch/stefan/7916125/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043271 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [42, 22, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 1, 1, 42, 42, 42, 22, 22, 1, 1, 1, 1, 1, 5, 14, 1, 3, 1, 1] 168
rigid atoms, others: [33, 3, 36, 5, 6, 7, 8, 9, 18, 19, 20, 26, 27, 28, 29, 30, 35] set([0, 1, 2, 34, 4, 32, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 31])
total number of confs: 169
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043271 none C=CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 38, 14, 38, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 14, 14, 56, 56, 56, 56, 56, 14, 14, 14, 14, 14, 6, 1, 14, 42, 14, 14] 168
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 239
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043271 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043271
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043271/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043271
Building REAL250005043272
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043272'
/scratch/stefan/7916125/working/building/REAL250005043272 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043272

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043272/0 /scratch/stefan/7916125/working/building/REAL250005043272 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/380
`/scratch/stefan/7916125/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043272 none N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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: [26, 26, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 1, 1, 26, 26, 1, 1, 1, 1, 1, 5, 12, 1, 3, 1, 1] 132
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 18, 19, 20, 23, 24, 25, 26, 27, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 28, 29, 31])
total number of confs: 114
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043272 none N#CCC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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: [44, 44, 32, 12, 32, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 44, 12, 12, 12, 12, 12, 6, 1, 12, 36, 12, 12] 132
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 185
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043272 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043272
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043272/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043272
Building REAL250005043273
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043273'
/scratch/stefan/7916125/working/building/REAL250005043273 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043273

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043273/0 /scratch/stefan/7916125/working/building/REAL250005043273 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/381
`/scratch/stefan/7916125/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:2-3 Rotatable hydrogens  reported. Reducing confs by a factor of 3
WARNING:root:Setting energy window to 12 and max confs to 66
('energy: ', 12.0)
('conf: ', 66)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043273 none C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 16, 16, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 1, 1, 16, 16, 16, 48, 1, 1, 1, 1, 1, 5, 10, 1, 3, 1, 1] 225
rigid atoms, others: [33, 35, 4, 6, 7, 8, 9, 10, 19, 20, 21, 36, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 34, 31])
total number of confs: 126
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043273 none C[C@@H](O)C(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
2  hydrogens need rotated
225  conformations in input
total number of sets (complete confs): 225
using faster count positions algorithm for large data
unique positions, atoms: [25, 22, 25, 25, 10, 22, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 25, 25, 75, 10, 10, 10, 10, 10, 7, 1, 10, 30, 10, 10] 225
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 180
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043273 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043273
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043273/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043273
Building REAL250005043274
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043274'
/scratch/stefan/7916125/working/building/REAL250005043274 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043274

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043274/0 /scratch/stefan/7916125/working/building/REAL250005043274 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/382
`/scratch/stefan/7916125/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1)

`REAL250005043274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043274 none C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [15, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 15, 15, 15, 1, 1, 1, 1, 1, 6, 14, 1, 4, 1, 1] 81
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 17, 18, 19, 23, 24, 25, 26, 27, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 28, 29, 31])
total number of confs: 71
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043274 none C=CC(=O)N1CCC(NC(=O)C2=CC(=O)[N-]O2)C(O)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [27, 27, 14, 27, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 27, 27, 27, 14, 14, 14, 14, 14, 8, 1, 14, 42, 14, 14] 81
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 119
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043274 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043274
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043274/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043274
Building REAL250005043275
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043275'
/scratch/stefan/7916125/working/building/REAL250005043275 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043275

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043275/0 /scratch/stefan/7916125/working/building/REAL250005043275 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/383
`/scratch/stefan/7916125/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043275 none CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [146, 53, 53, 53, 10, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 1, 146, 146, 146, 146, 146, 53, 10, 10, 1, 1, 1, 1, 6, 30, 1, 1] 198
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 570
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043275 none CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
198  conformations in input
total number of sets (complete confs): 198
using faster count positions algorithm for large data
unique positions, atoms: [198, 158, 158, 158, 98, 30, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 198, 198, 198, 198, 198, 158, 98, 98, 30, 30, 30, 30, 9, 1, 30, 30] 198
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 774
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043275 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043275
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043275/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043275
Building REAL250005043276
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043276'
/scratch/stefan/7916125/working/building/REAL250005043276 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043276

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043276/0 /scratch/stefan/7916125/working/building/REAL250005043276 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/384
`/scratch/stefan/7916125/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043276 none COCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [170, 149, 130, 36, 36, 36, 7, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 170, 170, 170, 149, 149, 130, 130, 36, 7, 7, 1, 1, 1, 1, 6, 13, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 629
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043276 none COCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 115, 115, 115, 43, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 201, 201, 201, 201, 201, 195, 195, 115, 43, 43, 13, 13, 13, 13, 4, 1, 13, 13] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 769
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043276 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043276
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043276/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043276
Building REAL250005043277
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043277'
/scratch/stefan/7916125/working/building/REAL250005043277 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043277

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043277/0 /scratch/stefan/7916125/working/building/REAL250005043277 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/385
`/scratch/stefan/7916125/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043277 none CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [36, 36, 36, 10, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 36, 36, 36, 36, 10, 10, 1, 1, 1, 1, 6, 20, 1, 1] 58
rigid atoms, others: [4, 5, 6, 7, 8, 17, 24, 25, 26, 27, 30, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 28, 29])
total number of confs: 130
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043277 none CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 49, 20, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 58, 58, 58, 58, 49, 49, 20, 20, 20, 20, 7, 1, 20, 20] 58
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 209
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043277 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043277
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043277/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043277
Building REAL250005043278
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043278'
/scratch/stefan/7916125/working/building/REAL250005043278 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043278

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043278/0 /scratch/stefan/7916125/working/building/REAL250005043278 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/386
`/scratch/stefan/7916125/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043278 none O=C(NC1CC(CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 47, 47, 47, 159, 159, 1, 6, 17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 9, 9, 47, 159, 159, 159, 159, 159, 1, 1, 17] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 13, 34, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 458
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043278 none O=C(NC1CC(CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 154, 154, 154, 64, 11, 11, 1, 11, 1, 1, 1, 154, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 64, 64, 11, 1, 1, 1, 1, 1, 154, 154, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 636
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: REAL250005043278 none O=C(NC1CC(CNC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 17, 17, 17, 69, 151, 151, 151, 201, 201, 17, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 69, 69, 151, 201, 201, 201, 201, 201, 17, 17, 1] 201
rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 660
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043278 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043278
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043278/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043278
Building REAL250005043279
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043279'
/scratch/stefan/7916125/working/building/REAL250005043279 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043279

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043279/0 /scratch/stefan/7916125/working/building/REAL250005043279 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/387
`/scratch/stefan/7916125/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043279 none O=C(NC1CC(CNC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 53, 53, 53, 158, 158, 158, 1, 6, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 9, 9, 53, 158, 158, 158, 158, 158, 158, 158, 1, 1, 18] 201
rigid atoms, others: [2, 3, 4, 5, 6, 14, 22, 23, 24, 25, 37, 36] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 463
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043279 none O=C(NC1CC(CNC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 158, 158, 59, 11, 11, 1, 11, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 59, 59, 11, 1, 1, 1, 1, 1, 1, 1, 158, 158, 201] 201
rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38])
total number of confs: 636
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: REAL250005043279 none O=C(NC1CC(CNC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 67, 147, 147, 147, 201, 201, 201, 18, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 67, 67, 147, 201, 201, 201, 201, 201, 201, 201, 18, 18, 1] 201
rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 659
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043279 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043279
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043279/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043279
Building REAL250005043280
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043280'
/scratch/stefan/7916125/working/building/REAL250005043280 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043280

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043280/0 /scratch/stefan/7916125/working/building/REAL250005043280 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/388
`/scratch/stefan/7916125/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043280 none O=C(CC1CC1)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 3, 1, 1, 1, 1, 22, 22, 100, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 173, 3, 3, 1, 1, 1, 1, 1, 22, 100, 100, 173, 173, 173, 173, 201, 201, 173, 173] 201
rigid atoms, others: [2, 3, 4, 5, 23, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 696
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043280 none O=C(CC1CC1)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 145, 173, 173, 7, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 145, 145, 173, 173, 173, 173, 173, 38, 7, 7, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 648
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043280 none O=C(CC1CC1)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 191, 201, 201, 40, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 191, 191, 201, 201, 201, 201, 201, 125, 40, 40, 12, 12, 12, 12, 3, 1, 12, 12] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 768
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043280 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043280
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043280/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043280
Building REAL250005043281
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043281'
/scratch/stefan/7916125/working/building/REAL250005043281 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043281

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043281/0 /scratch/stefan/7916125/working/building/REAL250005043281 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/389
`/scratch/stefan/7916125/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043281 none CC(C)(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 51, 153, 153, 51, 51, 9, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 153, 153, 153, 153, 153, 153, 51, 9, 9, 1, 1, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 582
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043281 none CC(C)(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 155, 201, 201, 155, 155, 67, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 155, 67, 67, 20, 20, 20, 20, 6, 1, 20, 20] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 737
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043281 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043281
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043281/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043281
Building REAL250005043282
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043282'
/scratch/stefan/7916125/working/building/REAL250005043282 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043282

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043282/0 /scratch/stefan/7916125/working/building/REAL250005043282 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/390
`/scratch/stefan/7916125/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043282 none COCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [150, 113, 42, 42, 42, 7, 1, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 1, 150, 150, 150, 119, 119, 42, 7, 7, 1, 1, 1, 1, 6, 24, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 533
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043282 none COCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 173, 173, 173, 81, 24, 24, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 201, 201, 201, 201, 201, 173, 81, 81, 24, 24, 24, 24, 6, 1, 24, 24] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043282 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043282
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043282/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043282
Building REAL250005043283
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043283'
/scratch/stefan/7916125/working/building/REAL250005043283 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043283

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043283/0 /scratch/stefan/7916125/working/building/REAL250005043283 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/391
`/scratch/stefan/7916125/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043283 none CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 141, 39, 39, 39, 7, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 161, 161, 161, 161, 161, 141, 141, 39, 7, 7, 1, 1, 1, 1, 6, 11, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 699
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043283 none CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 128, 128, 128, 44, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 201, 201, 196, 196, 128, 44, 44, 11, 11, 11, 11, 4, 1, 11, 11] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 760
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043283 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043283
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043283/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043283
Building REAL250005043284
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043284'
/scratch/stefan/7916125/working/building/REAL250005043284 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043284

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043284/0 /scratch/stefan/7916125/working/building/REAL250005043284 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/392
`/scratch/stefan/7916125/working/3D/392' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043284 none CC(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 139, 155, 49, 49, 49, 9, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 155, 155, 155, 155, 155, 155, 155, 139, 139, 49, 9, 9, 1, 1, 1, 1, 6, 17, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 720
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043284 none CC(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 140, 140, 140, 62, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 62, 62, 17, 17, 17, 17, 6, 1, 17, 17] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 732
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043284 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043284
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043284/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043284
Building REAL250005043285
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043285'
/scratch/stefan/7916125/working/building/REAL250005043285 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043285

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043285/0 /scratch/stefan/7916125/working/building/REAL250005043285 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/393
`/scratch/stefan/7916125/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043285 none CC1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 54, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 153, 2, 2, 2, 1, 1, 1, 1, 10, 54, 54, 153, 153, 153, 153, 201, 201, 153, 153] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 641
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043285 none CC1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 153, 54, 54, 54, 9, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 153, 153, 153, 153, 153, 153, 153, 54, 9, 9, 1, 1, 1, 1, 6, 20, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 449
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: REAL250005043285 none CC1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 159, 159, 159, 75, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 20, 201, 201, 201, 201, 201, 201, 201, 159, 75, 75, 20, 20, 20, 20, 6, 1, 20, 20] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 671
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043285 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043285
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043285/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043285
Building REAL250005043286
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043286'
/scratch/stefan/7916125/working/building/REAL250005043286 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043286

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043286/0 /scratch/stefan/7916125/working/building/REAL250005043286 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/394
`/scratch/stefan/7916125/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043286 none CCOCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 153, 90, 36, 36, 36, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 159, 159, 159, 159, 159, 93, 93, 36, 7, 7, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 519
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043286 none CCOCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 189, 133, 133, 133, 46, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 190, 190, 133, 46, 46, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 724
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043286 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043286
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043286/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043286
Building REAL250005043287
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043287'
/scratch/stefan/7916125/working/building/REAL250005043287 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043287

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043287/0 /scratch/stefan/7916125/working/building/REAL250005043287 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/395
`/scratch/stefan/7916125/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043287 none CC(C)=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [134, 134, 134, 54, 54, 54, 10, 1, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 30, 30, 1, 134, 134, 134, 134, 134, 134, 134, 54, 10, 10, 1, 1, 1, 1, 6, 30, 1, 1] 197
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 428
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043287 none CC(C)=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [197, 197, 197, 165, 165, 165, 89, 30, 30, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 197, 197, 197, 197, 197, 197, 197, 165, 89, 89, 30, 30, 30, 30, 9, 1, 30, 30] 197
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 668
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043287 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043287
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043287/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043287
Building REAL250005043288
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043288'
/scratch/stefan/7916125/working/building/REAL250005043288 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043288

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043288/0 /scratch/stefan/7916125/working/building/REAL250005043288 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/396
`/scratch/stefan/7916125/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043288 none CSCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [167, 114, 30, 30, 30, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 167, 167, 167, 114, 114, 30, 7, 7, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 530
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043288 none CSCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 117, 117, 117, 48, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 184, 184, 117, 48, 48, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 710
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043288 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043288
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043288/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043288
Building REAL250005043289
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043289'
/scratch/stefan/7916125/working/building/REAL250005043289 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043289

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043289/0 /scratch/stefan/7916125/working/building/REAL250005043289 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/397
`/scratch/stefan/7916125/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043289 none CCCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 138, 125, 29, 29, 29, 6, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 157, 157, 157, 157, 157, 152, 152, 125, 125, 29, 6, 6, 1, 1, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 742
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043289 none CCCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 189, 100, 100, 100, 28, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 201, 200, 200, 189, 189, 100, 28, 28, 10, 10, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 777
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043289 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043289
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043289/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043289
Building REAL250005043290
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043290'
/scratch/stefan/7916125/working/building/REAL250005043290 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043290

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043290/0 /scratch/stefan/7916125/working/building/REAL250005043290 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/398
`/scratch/stefan/7916125/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043290 none CC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 53, 144, 53, 53, 9, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 144, 144, 144, 144, 144, 144, 144, 53, 9, 9, 1, 1, 1, 1, 6, 23, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 6, 7, 8, 9, 10, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 559
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043290 none CC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 174, 201, 174, 174, 89, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 201, 201, 174, 89, 89, 23, 23, 23, 23, 7, 1, 23, 23] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 733
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043290 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043290
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043290/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043290
Building REAL250005043291
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043291'
/scratch/stefan/7916125/working/building/REAL250005043291 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043291

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043291/0 /scratch/stefan/7916125/working/building/REAL250005043291 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/399
`/scratch/stefan/7916125/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043291 none CCC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 127, 39, 127, 39, 39, 9, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 147, 147, 147, 147, 147, 127, 127, 127, 127, 39, 9, 9, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 614
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043291 none CCC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 124, 200, 124, 124, 47, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 200, 200, 200, 200, 124, 47, 47, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 747
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043291 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043291
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043291/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043291
Building REAL250005043292
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043292'
/scratch/stefan/7916125/working/building/REAL250005043292 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043292

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043292/0 /scratch/stefan/7916125/working/building/REAL250005043292 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/400
`/scratch/stefan/7916125/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043292 none COC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 123, 47, 130, 47, 47, 9, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 157, 157, 157, 130, 130, 130, 130, 47, 9, 9, 1, 1, 1, 1, 6, 22, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 562
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043292 none COC(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 166, 200, 166, 166, 74, 22, 22, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 200, 200, 200, 200, 166, 74, 74, 22, 22, 22, 22, 7, 1, 22, 22] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 735
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043292 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043292
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043292/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043292
Building REAL250005043293
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043293'
/scratch/stefan/7916125/working/building/REAL250005043293 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043293

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043293/0 /scratch/stefan/7916125/working/building/REAL250005043293 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/401
`/scratch/stefan/7916125/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043293 none C=CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [175, 138, 123, 28, 28, 28, 6, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 175, 175, 175, 138, 138, 123, 123, 28, 6, 6, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 690
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043293 none C=CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 189, 107, 107, 107, 42, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 189, 189, 107, 42, 42, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 809
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043293 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043293
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043293/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043293
Building REAL250005043294
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043294'
/scratch/stefan/7916125/working/building/REAL250005043294 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043294

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043294/0 /scratch/stefan/7916125/working/building/REAL250005043294 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/402
`/scratch/stefan/7916125/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043294 none CC=C(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 52, 155, 52, 52, 9, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 1, 155, 155, 155, 155, 155, 155, 155, 52, 9, 9, 1, 1, 1, 1, 6, 18, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 445
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043294 none CC=C(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 148, 201, 148, 148, 62, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 201, 201, 201, 201, 201, 201, 201, 148, 62, 62, 18, 18, 18, 18, 6, 1, 18, 18] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 663
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043294 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043294
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043294/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043294
Building REAL250005043295
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043295'
/scratch/stefan/7916125/working/building/REAL250005043295 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043295

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043295/0 /scratch/stefan/7916125/working/building/REAL250005043295 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/403
`/scratch/stefan/7916125/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NCC2CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005043295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043295 none CC1(C(=O)NCC2CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 46, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 1, 1, 2, 2, 2, 7, 46, 46, 135, 135, 135, 135, 201, 201, 135, 135, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 644
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043295 none CC1(C(=O)NCC2CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 43, 43, 9, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 135, 135, 135, 135, 135, 43, 9, 9, 1, 1, 1, 1, 6, 17, 1, 1, 135, 135, 135, 135] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 35, 36, 37, 38])
total number of confs: 398
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: REAL250005043295 none CC1(C(=O)NCC2CC(NC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 60, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 113, 60, 60, 17, 17, 17, 17, 5, 1, 17, 17, 201, 201, 201, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 650
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043295 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043295
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043295/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043295
Building REAL250005043296
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043296'
/scratch/stefan/7916125/working/building/REAL250005043296 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043296

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043296/0 /scratch/stefan/7916125/working/building/REAL250005043296 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/404
`/scratch/stefan/7916125/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043296 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 2, 2, 2, 1, 1, 12, 66, 66, 159, 159, 159, 159, 201, 201, 159, 159] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 651
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043296 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 45, 159, 45, 45, 9, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 159, 159, 159, 159, 159, 45, 9, 9, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 447
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043296 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 128, 201, 128, 128, 51, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 128, 51, 51, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 639
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043296 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043296
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043296/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043296
Building REAL250005043297
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043297'
/scratch/stefan/7916125/working/building/REAL250005043297 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043297

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043297/0 /scratch/stefan/7916125/working/building/REAL250005043297 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/405
`/scratch/stefan/7916125/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043297 none CCC(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [152, 130, 43, 130, 43, 43, 9, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 164, 164, 164, 164, 164, 130, 43, 9, 9, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 763
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043297 none CCC(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 192, 132, 192, 132, 132, 47, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 192, 132, 47, 47, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043297 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043297
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043297/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043297
Building REAL250005043298
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043298'
/scratch/stefan/7916125/working/building/REAL250005043298 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043298

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043298/0 /scratch/stefan/7916125/working/building/REAL250005043298 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/406
`/scratch/stefan/7916125/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043298 none O=C(CCCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 123, 120, 169, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 123, 123, 150, 150, 154, 157, 28, 6, 6, 1, 1, 1, 1, 6, 6, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 823
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043298 none O=C(CCCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 88, 88, 190, 195, 201, 22, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 190, 190, 201, 201, 201, 201, 88, 22, 22, 6, 6, 6, 6, 2, 1, 6, 6] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 806
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043298 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043298
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043298/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043298
Building REAL250005043299
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043299'
/scratch/stefan/7916125/working/building/REAL250005043299 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043299

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043299/0 /scratch/stefan/7916125/working/building/REAL250005043299 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/407
`/scratch/stefan/7916125/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043299 none C[C@H]1C[C@@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 65, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 201, 143, 2, 2, 2, 1, 1, 13, 65, 65, 143, 143, 143, 143, 201, 201, 143, 143] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 676
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043299 none C[C@H]1C[C@@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 143, 44, 143, 44, 44, 9, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 143, 143, 143, 143, 143, 44, 9, 9, 1, 1, 1, 1, 6, 17, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 422
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: REAL250005043299 none C[C@H]1C[C@@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 139, 201, 139, 139, 63, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 139, 63, 63, 17, 17, 17, 17, 6, 1, 17, 17] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 649
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043299 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043299
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043299/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043299
Building REAL250005043300
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043300'
/scratch/stefan/7916125/working/building/REAL250005043300 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043300

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043300/0 /scratch/stefan/7916125/working/building/REAL250005043300 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/408
`/scratch/stefan/7916125/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043300 none NC(=O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [91, 52, 95, 52, 52, 10, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 91, 95, 52, 10, 10, 1, 1, 1, 1, 6, 25, 1, 1] 146
rigid atoms, others: [32, 6, 7, 8, 9, 10, 19, 25, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 312
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043300 none NC(=O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
146  conformations in input
total number of sets (complete confs): 146
using faster count positions algorithm for large data
unique positions, atoms: [144, 136, 146, 136, 136, 83, 25, 25, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 144, 146, 136, 83, 83, 25, 25, 25, 25, 9, 1, 25, 25] 146
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 502
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043300 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043300
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043300/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043300
Building REAL250005043301
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043301'
/scratch/stefan/7916125/working/building/REAL250005043301 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043301

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043301/0 /scratch/stefan/7916125/working/building/REAL250005043301 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/409
`/scratch/stefan/7916125/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043301 none CC(C)(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [67, 50, 67, 67, 50, 50, 10, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 50, 10, 10, 1, 1, 1, 1, 6, 25, 1, 1] 102
rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 40, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 265
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043301 none CC(C)(C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 90, 102, 102, 90, 90, 61, 25, 25, 25, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 25, 102, 102, 102, 102, 102, 102, 102, 102, 102, 90, 61, 61, 25, 25, 25, 25, 6, 1, 25, 25] 102
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 380
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043301 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043301
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043301/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043301
Building REAL250005043302
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043302'
/scratch/stefan/7916125/working/building/REAL250005043302 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043302

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043302/0 /scratch/stefan/7916125/working/building/REAL250005043302 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/410
`/scratch/stefan/7916125/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043302 none C=CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [168, 111, 32, 32, 32, 7, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 168, 168, 168, 111, 111, 32, 7, 7, 1, 1, 1, 1, 6, 23, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 631
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043302 none C=CCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 147, 147, 147, 70, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 147, 70, 70, 23, 23, 23, 23, 6, 1, 23, 23] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 762
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043302 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043302
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043302/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043302
Building REAL250005043303
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043303'
/scratch/stefan/7916125/working/building/REAL250005043303 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043303

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043303/0 /scratch/stefan/7916125/working/building/REAL250005043303 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/411
`/scratch/stefan/7916125/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043303 none C[NH+](C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [105, 104, 105, 105, 46, 46, 46, 9, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 105, 105, 105, 105, 105, 105, 104, 104, 46, 9, 9, 1, 1, 1, 1, 6, 17, 1, 1] 136
rigid atoms, others: [33, 34, 35, 36, 39, 8, 9, 10, 11, 12, 40, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38])
total number of confs: 417
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043303 none C[NH+](C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
136  conformations in input
total number of sets (complete confs): 136
using faster count positions algorithm for large data
unique positions, atoms: [136, 136, 136, 136, 110, 110, 110, 49, 17, 17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 136, 136, 136, 136, 136, 136, 136, 136, 110, 49, 49, 17, 17, 17, 17, 9, 1, 17, 17] 136
rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 493
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043303 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043303/1 /scratch/stefan/7916125/working/building/REAL250005043303 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/412
`/scratch/stefan/7916125/working/3D/412' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043303.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043303/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043303 none CN(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 114, 129, 48, 48, 48, 9, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 1, 129, 129, 129, 129, 129, 129, 114, 114, 48, 9, 9, 1, 1, 1, 1, 6, 21, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 38, 7, 8, 9, 10, 11, 20, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37])
total number of confs: 511
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043303 none CN(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 153, 153, 76, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 201, 201, 201, 201, 153, 76, 76, 21, 21, 21, 21, 7, 1, 21, 21] 201
rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 760
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043303 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043303
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043303/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043303/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043303
Building REAL250005043304
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043304'
/scratch/stefan/7916125/working/building/REAL250005043304 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043304

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043304/0 /scratch/stefan/7916125/working/building/REAL250005043304 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/413
`/scratch/stefan/7916125/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043304 none C=CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 107, 38, 107, 38, 38, 7, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 162, 162, 162, 107, 321, 38, 7, 7, 1, 1, 1, 1, 6, 23, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 939
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043304 none C=CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 151, 151, 64, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 603, 151, 64, 64, 23, 23, 23, 23, 6, 1, 23, 23] 603
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1334
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043304 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043304
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043304/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043304
Building REAL250005043305
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043305'
/scratch/stefan/7916125/working/building/REAL250005043305 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043305

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043305/0 /scratch/stefan/7916125/working/building/REAL250005043305 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/414
`/scratch/stefan/7916125/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2COC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043305 none O=C(NC1CC(CNC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 9, 51, 51, 51, 158, 158, 158, 1, 6, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 9, 9, 51, 158, 158, 158, 158, 158, 1, 1, 20] 201
rigid atoms, others: [2, 3, 4, 5, 6, 34, 14, 35, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 453
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043305 none O=C(NC1CC(CNC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 158, 158, 70, 13, 13, 1, 13, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 70, 70, 13, 1, 1, 1, 1, 1, 158, 158, 201] 201
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 670
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: REAL250005043305 none O=C(NC1CC(CNC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 70, 146, 146, 146, 201, 201, 201, 20, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 70, 70, 146, 201, 201, 201, 201, 201, 20, 20, 1] 201
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 656
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043305 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043305
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043305/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043305
Building REAL250005043306
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043306'
/scratch/stefan/7916125/working/building/REAL250005043306 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043306

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043306/0 /scratch/stefan/7916125/working/building/REAL250005043306 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/415
`/scratch/stefan/7916125/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043306 none CO[C@H](C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [156, 121, 47, 129, 129, 47, 47, 9, 1, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 1, 156, 156, 156, 129, 129, 129, 47, 9, 9, 1, 1, 1, 1, 6, 22, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 8, 9, 10, 11, 12, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 561
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043306 none CO[C@H](C)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 166, 200, 200, 166, 166, 74, 22, 22, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 22, 201, 201, 201, 200, 200, 200, 166, 74, 74, 22, 22, 22, 22, 7, 1, 22, 22] 201
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043306 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043306
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043306/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043306
Building REAL250005043307
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043307'
/scratch/stefan/7916125/working/building/REAL250005043307 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043307

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043307/0 /scratch/stefan/7916125/working/building/REAL250005043307 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/416
`/scratch/stefan/7916125/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043307 none CCC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 121, 119, 37, 37, 37, 7, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 165, 165, 165, 165, 165, 121, 121, 37, 7, 7, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 611
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043307 none CCC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 177, 140, 140, 140, 51, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 177, 177, 140, 51, 51, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 709
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043307 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043307
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043307/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043307
Building REAL250005043308
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043308'
/scratch/stefan/7916125/working/building/REAL250005043308 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005043308 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005043308' -> `/scratch/stefan/7916125/failed/REAL250005043308'
Building REAL250005043309
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043309'
/scratch/stefan/7916125/working/building/REAL250005043309 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043309

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043309/0 /scratch/stefan/7916125/working/building/REAL250005043309 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/417
`/scratch/stefan/7916125/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043309 none O=C(CO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
393  conformations in input
total number of sets (complete confs): 393
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 98, 10, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 98, 98, 294, 47, 10, 10, 1, 1, 1, 1, 6, 26, 1, 1] 393
rigid atoms, others: [32, 5, 6, 7, 8, 9, 18, 25, 26, 27, 28, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30])
total number of confs: 688
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043309 none O=C(CO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
393  conformations in input
total number of sets (complete confs): 393
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 131, 75, 26, 26, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 131, 131, 393, 128, 75, 75, 26, 26, 26, 26, 9, 1, 26, 26] 393
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 841
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043309 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043309
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043309/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043309
Building REAL250005043310
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043310'
/scratch/stefan/7916125/working/building/REAL250005043310 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043310

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043310/0 /scratch/stefan/7916125/working/building/REAL250005043310 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/418
`/scratch/stefan/7916125/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043310 none CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 52, 158, 52, 52, 10, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 1, 162, 162, 162, 162, 486, 52, 10, 10, 1, 1, 1, 1, 6, 29, 1, 1] 603
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 1111
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043310 none CC(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 187, 201, 187, 187, 95, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 201, 201, 201, 201, 603, 187, 95, 95, 29, 29, 29, 29, 9, 1, 29, 29] 603
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1292
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043310 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043310
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043310/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043310
Building REAL250005043311
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043311'
/scratch/stefan/7916125/working/building/REAL250005043311 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043311

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043311/0 /scratch/stefan/7916125/working/building/REAL250005043311 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/419
`/scratch/stefan/7916125/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1)

`REAL250005043311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043311 none O=C(NC1CC(CNC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 54, 54, 54, 160, 160, 160, 1, 6, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 9, 9, 54, 160, 160, 160, 160, 1, 1, 18] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 34, 14, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 463
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043311 none O=C(NC1CC(CNC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 160, 160, 160, 72, 12, 12, 1, 12, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 72, 72, 12, 1, 1, 1, 1, 160, 160, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 652
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: REAL250005043311 none O=C(NC1CC(CNC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 5, 18, 18, 18, 66, 151, 151, 151, 201, 201, 201, 18, 1, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 66, 66, 151, 201, 201, 201, 201, 18, 18, 1] 201
rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 640
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043311 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043311
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043311/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043311
Building REAL250005043312
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043312'
/scratch/stefan/7916125/working/building/REAL250005043312 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043312

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043312/0 /scratch/stefan/7916125/working/building/REAL250005043312 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/420
`/scratch/stefan/7916125/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043312 none O=C(CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 140, 164, 9, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 1, 140, 140, 164, 164, 41, 9, 9, 1, 1, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 31, 32])
total number of confs: 646
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043312 none O=C(CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 201, 201, 201, 201, 118, 40, 40, 10, 10, 10, 10, 4, 1, 10, 10] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 744
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043312 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043312
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043312/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043312
Building REAL250005043313
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043313'
/scratch/stefan/7916125/working/building/REAL250005043313 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043313

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043313/0 /scratch/stefan/7916125/working/building/REAL250005043313 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/421
`/scratch/stefan/7916125/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043313 none O=C(C=CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 104, 104, 179, 7, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 104, 104, 179, 179, 34, 7, 7, 1, 1, 1, 1, 6, 15, 1, 1] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 673
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043313 none O=C(C=CCF)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 199, 199, 201, 52, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 199, 199, 201, 201, 144, 52, 52, 15, 15, 15, 15, 4, 1, 15, 15] 201
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 643
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043313 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043313
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043313/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043313
Building REAL250005043314
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043314'
/scratch/stefan/7916125/working/building/REAL250005043314 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043314

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043314/0 /scratch/stefan/7916125/working/building/REAL250005043314 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/422
`/scratch/stefan/7916125/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043314 none C#CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [153, 153, 129, 36, 36, 36, 7, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 153, 153, 153, 129, 129, 36, 7, 7, 1, 1, 1, 1, 6, 11, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 606
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043314 none C#CCCC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 187, 107, 107, 107, 33, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 201, 201, 201, 187, 187, 107, 33, 33, 11, 11, 11, 11, 4, 1, 11, 11] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 766
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043314 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043314
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043314/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043314
Building REAL250005043315
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043315'
/scratch/stefan/7916125/working/building/REAL250005043315 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043315

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043315/0 /scratch/stefan/7916125/working/building/REAL250005043315 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/423
`/scratch/stefan/7916125/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1)

`REAL250005043315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043315 none O=C(NC1CC(CNC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 54, 54, 54, 128, 128, 128, 1, 6, 28, 28, 28, 28, 28, 6, 1, 1, 1, 1, 10, 10, 54, 128, 128, 128, 128, 128, 1, 1, 28] 178
rigid atoms, others: [2, 3, 4, 5, 6, 34, 14, 35, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 392
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043315 none O=C(NC1CC(CNC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 128, 128, 128, 59, 11, 11, 1, 11, 1, 1, 1, 1, 128, 167, 178, 178, 178, 178, 178, 167, 128, 128, 128, 128, 59, 59, 11, 1, 1, 1, 1, 1, 128, 128, 178] 178
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 564
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: REAL250005043315 none O=C(NC1CC(CNC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
178  conformations in input
total number of sets (complete confs): 178
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 8, 8, 28, 28, 28, 88, 156, 156, 156, 178, 178, 178, 28, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 28, 88, 88, 156, 178, 178, 178, 178, 178, 28, 28, 1] 178
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 590
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043315 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043315
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043315/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043315
Building REAL250005043316
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043316'
/scratch/stefan/7916125/working/building/REAL250005043316 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043316

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043316/0 /scratch/stefan/7916125/working/building/REAL250005043316 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/424
`/scratch/stefan/7916125/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043316 none CC(C)(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [153, 54, 153, 151, 54, 54, 10, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 153, 153, 153, 153, 153, 153, 459, 54, 10, 10, 1, 1, 1, 1, 6, 23, 1, 1] 603
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 1045
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043316 none CC(C)(O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 172, 201, 201, 172, 172, 76, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 23, 201, 201, 201, 201, 201, 201, 603, 172, 76, 76, 23, 23, 23, 23, 6, 1, 23, 23] 603
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1306
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043316 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043316
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043316/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043316
Building REAL250005043317
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043317'
/scratch/stefan/7916125/working/building/REAL250005043317 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043317

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043317/0 /scratch/stefan/7916125/working/building/REAL250005043317 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/425
`/scratch/stefan/7916125/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043317 none CC1=CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 77, 166, 166, 166, 201, 201, 201, 201, 201, 201, 201, 201, 166, 2, 2, 2, 1, 1, 13, 77, 77, 166, 166, 166, 166, 201, 201, 166, 166] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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])
total number of confs: 685
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043317 none CC1=CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [166, 166, 166, 46, 46, 46, 9, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 166, 166, 166, 166, 166, 46, 9, 9, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 453
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043317 none CC1=CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 52, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 127, 52, 52, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 632
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043317 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043317
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043317/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043317
Building REAL250005043318
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043318'
/scratch/stefan/7916125/working/building/REAL250005043318 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043318

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043318/0 /scratch/stefan/7916125/working/building/REAL250005043318 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/426
`/scratch/stefan/7916125/working/3D/426' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043318 none C[C@@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [159, 53, 159, 153, 53, 53, 10, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 1, 159, 159, 159, 477, 53, 10, 10, 1, 1, 1, 1, 6, 29, 1, 1] 603
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 1084
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043318 none C[C@@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 187, 201, 201, 187, 187, 95, 29, 29, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 201, 201, 201, 603, 187, 95, 95, 29, 29, 29, 29, 8, 1, 29, 29] 603
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1295
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043318 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043318
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043318/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043318
Building REAL250005043319
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043319'
/scratch/stefan/7916125/working/building/REAL250005043319 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043319

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043319/0 /scratch/stefan/7916125/working/building/REAL250005043319 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/427
`/scratch/stefan/7916125/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043319 none O=C(C=CCO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 33, 33, 97, 97, 168, 7, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 97, 97, 168, 168, 504, 33, 7, 7, 1, 1, 1, 1, 6, 15, 1, 1] 603
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 1148
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043319 none O=C(C=CCO)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 194, 194, 201, 50, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 15, 194, 194, 201, 201, 603, 135, 50, 50, 15, 15, 15, 15, 4, 1, 15, 15] 603
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1254
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043319 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043319
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043319/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043319
Building REAL250005043320
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043320'
/scratch/stefan/7916125/working/building/REAL250005043320 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043320

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043320/0 /scratch/stefan/7916125/working/building/REAL250005043320 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/428
`/scratch/stefan/7916125/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005043320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043320 none O=C(NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 10, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 48, 67, 67, 67, 48, 10, 10, 1, 1, 1, 1, 6, 23, 1, 1, 67, 67, 67, 67, 67] 92
rigid atoms, others: [3, 4, 5, 6, 7, 16, 24, 25, 26, 27, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 192
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043320 none O=C(NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 61, 23, 23, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 92, 92, 92, 92, 92, 61, 61, 23, 23, 23, 23, 8, 1, 23, 23, 92, 92, 92, 92, 92] 92
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 313
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: REAL250005043320 none O=C(NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 37, 67, 67, 67, 88, 88, 88, 92, 92, 92, 92, 92, 67, 1, 1, 1, 1, 10, 37, 37, 67, 67, 67, 67, 88, 92, 67, 67, 1, 1, 1, 1, 1] 92
rigid atoms, others: [32, 1, 34, 35, 36, 33, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 292
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043320 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043320
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043320/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043320
Building REAL250005043321
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043321'
/scratch/stefan/7916125/working/building/REAL250005043321 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043321

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043321/0 /scratch/stefan/7916125/working/building/REAL250005043321 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/429
`/scratch/stefan/7916125/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043321 none CON=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [109, 92, 92, 41, 41, 41, 7, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 109, 109, 109, 92, 41, 7, 7, 1, 1, 1, 1, 6, 25, 1, 1] 138
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 324
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043321 none CON=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 130, 130, 130, 71, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 138, 138, 138, 138, 130, 71, 71, 25, 25, 25, 25, 8, 1, 25, 25] 138
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 476
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043321 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043321
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043321/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043321
Building REAL250005043322
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043322'
/scratch/stefan/7916125/working/building/REAL250005043322 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043322

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043322/0 /scratch/stefan/7916125/working/building/REAL250005043322 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/430
`/scratch/stefan/7916125/working/3D/430' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043322 none O=C(NC1CC(CNC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 9, 51, 51, 51, 176, 176, 176, 1, 6, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 9, 9, 51, 176, 176, 176, 176, 1, 1, 12] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 34, 14, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 485
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043322 none O=C(NC1CC(CNC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 176, 176, 73, 12, 12, 1, 12, 1, 1, 1, 1, 176, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 73, 73, 12, 1, 1, 1, 1, 176, 176, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 646
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: REAL250005043322 none O=C(NC1CC(CNC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 12, 12, 12, 54, 155, 155, 155, 201, 201, 201, 12, 1, 1, 1, 1, 1, 1, 3, 12, 12, 12, 12, 54, 54, 155, 201, 201, 201, 201, 12, 12, 1] 201
rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 642
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043322 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043322
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043322/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043322
Building REAL250005043323
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043323'
/scratch/stefan/7916125/working/building/REAL250005043323 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043323

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043323/0 /scratch/stefan/7916125/working/building/REAL250005043323 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/431
`/scratch/stefan/7916125/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043323 none CC=C(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [124, 124, 49, 124, 49, 49, 10, 1, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 1, 124, 124, 124, 124, 49, 10, 10, 1, 1, 1, 1, 6, 25, 1, 1] 171
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 375
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043323 none CC=C(F)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [171, 171, 146, 171, 146, 146, 83, 25, 25, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 171, 171, 171, 171, 146, 83, 83, 25, 25, 25, 25, 9, 1, 25, 25] 171
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 563
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043323 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043323
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043323/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043323
Building REAL250005043324
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043324'
/scratch/stefan/7916125/working/building/REAL250005043324 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043324

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043324/0 /scratch/stefan/7916125/working/building/REAL250005043324 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/432
`/scratch/stefan/7916125/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043324 none CC(CO)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [112, 39, 112, 166, 39, 39, 7, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 112, 112, 112, 112, 166, 166, 498, 39, 7, 7, 1, 1, 1, 1, 6, 13, 1, 1] 603
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 1202
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043324 none CC(CO)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [196, 128, 196, 201, 128, 128, 48, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 196, 196, 196, 196, 201, 201, 603, 128, 48, 48, 13, 13, 13, 13, 4, 1, 13, 13] 603
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1353
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043324 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043324
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043324/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043324
Building REAL250005043325
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043325'
/scratch/stefan/7916125/working/building/REAL250005043325 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043325

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043325/0 /scratch/stefan/7916125/working/building/REAL250005043325 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/433
`/scratch/stefan/7916125/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043325 none C[C@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
600  conformations in input
total number of sets (complete confs): 600
using faster count positions algorithm for large data
unique positions, atoms: [149, 55, 149, 149, 55, 55, 10, 1, 1, 1, 1, 1, 6, 6, 6, 29, 29, 29, 29, 29, 1, 149, 149, 149, 447, 55, 10, 10, 1, 1, 1, 1, 6, 29, 1, 1] 600
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 1031
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043325 none C[C@H](O)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
600  conformations in input
total number of sets (complete confs): 600
using faster count positions algorithm for large data
unique positions, atoms: [200, 174, 200, 200, 174, 174, 90, 29, 29, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 200, 200, 200, 600, 174, 90, 90, 29, 29, 29, 29, 8, 1, 29, 29] 600
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1313
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043325 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043325
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043325/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043325
Building REAL250005043326
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043326'
/scratch/stefan/7916125/working/building/REAL250005043326 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043326

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043326/0 /scratch/stefan/7916125/working/building/REAL250005043326 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/434
`/scratch/stefan/7916125/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043326 none C=C1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 78, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 163, 1, 1, 1, 1, 1, 13, 78, 78, 163, 163, 163, 163, 201, 201, 163, 163] 201
rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([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])
total number of confs: 672
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043326 none C=C1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [163, 163, 163, 45, 45, 45, 9, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 163, 163, 163, 163, 163, 45, 9, 9, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 35, 36, 7, 8, 9, 10, 11, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34])
total number of confs: 449
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043326 none C=C1CC1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 140, 140, 140, 55, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 140, 55, 55, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 634
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043326 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043326
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043326/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043326
Building REAL250005043327
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043327'
/scratch/stefan/7916125/working/building/REAL250005043327 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043327

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043327/0 /scratch/stefan/7916125/working/building/REAL250005043327 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/435
`/scratch/stefan/7916125/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043327 none CC(CF)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 38, 114, 163, 38, 38, 7, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 114, 114, 114, 114, 163, 163, 38, 7, 7, 1, 1, 1, 1, 6, 12, 1, 1] 201
rigid atoms, others: [32, 33, 36, 37, 7, 8, 9, 10, 11, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35])
total number of confs: 686
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043327 none CC(CF)C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 123, 201, 201, 123, 123, 44, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 201, 201, 201, 201, 201, 201, 123, 44, 44, 12, 12, 12, 12, 4, 1, 12, 12] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 742
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043327 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043327
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043327/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043327
Building REAL250005043328
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043328'
/scratch/stefan/7916125/working/building/REAL250005043328 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043328

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043328/0 /scratch/stefan/7916125/working/building/REAL250005043328 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/436
`/scratch/stefan/7916125/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043328 none C=C(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [151, 117, 151, 31, 31, 31, 7, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 21, 1, 151, 151, 151, 151, 151, 117, 117, 31, 7, 7, 1, 1, 1, 1, 6, 21, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 7, 8, 9, 10, 11, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 563
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043328 none C=C(C)CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 201, 133, 133, 133, 64, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 201, 201, 201, 201, 201, 195, 195, 133, 64, 64, 21, 21, 21, 21, 6, 1, 21, 21] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 768
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043328 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043328
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043328/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043328
Building REAL250005043329
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043329'
/scratch/stefan/7916125/working/building/REAL250005043329 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043329

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043329/0 /scratch/stefan/7916125/working/building/REAL250005043329 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/437
`/scratch/stefan/7916125/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043329 none CC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [112, 112, 51, 51, 51, 10, 1, 1, 1, 1, 1, 6, 6, 6, 26, 26, 26, 26, 26, 1, 112, 112, 112, 112, 112, 51, 10, 10, 1, 1, 1, 1, 6, 26, 1, 1] 164
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33])
total number of confs: 360
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043329 none CC=CC(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 145, 145, 145, 87, 26, 26, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 164, 164, 164, 164, 164, 145, 87, 87, 26, 26, 26, 26, 8, 1, 26, 26] 164
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 564
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043329 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043329
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043329/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043329
Building REAL250005043330
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043330'
/scratch/stefan/7916125/working/building/REAL250005043330 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043330

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043330/0 /scratch/stefan/7916125/working/building/REAL250005043330 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/438
`/scratch/stefan/7916125/working/3D/438' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043330 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 159, 2, 2, 2, 1, 1, 12, 66, 66, 159, 159, 159, 159, 201, 201, 159, 159] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 651
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043330 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 159, 159, 45, 159, 45, 45, 9, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 159, 159, 159, 159, 159, 45, 9, 9, 1, 1, 1, 1, 6, 14, 1, 1] 201
rigid atoms, others: [32, 33, 34, 37, 38, 9, 10, 11, 12, 13, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36])
total number of confs: 447
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043330 none C[C@@H]1C[C@H]1C(=O)NCC1CC(NC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 128, 201, 128, 128, 51, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 201, 201, 201, 201, 201, 128, 51, 51, 14, 14, 14, 14, 4, 1, 14, 14] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 639
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043330 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043330
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043330/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043330
Building REAL250005043331
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043331'
/scratch/stefan/7916125/working/building/REAL250005043331 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043331

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043331/0 /scratch/stefan/7916125/working/building/REAL250005043331 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/439
`/scratch/stefan/7916125/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043331 none O=C(NC1CC(CNC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 163, 163, 163, 1, 6, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 9, 9, 51, 489, 163, 163, 163, 163, 1, 1, 14] 603
rigid atoms, others: [2, 3, 4, 5, 6, 34, 14, 35, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 952
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043331 none O=C(NC1CC(CNC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 163, 163, 163, 72, 12, 12, 1, 12, 1, 1, 1, 1, 163, 201, 201, 201, 201, 201, 201, 201, 163, 163, 163, 163, 72, 72, 12, 6, 1, 1, 1, 1, 163, 163, 201] 603
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 653
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: REAL250005043331 none O=C(NC1CC(CNC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 14, 14, 61, 155, 155, 155, 201, 201, 201, 14, 1, 1, 1, 1, 1, 1, 3, 14, 14, 14, 14, 61, 61, 155, 603, 201, 201, 201, 201, 14, 14, 1] 603
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 1253
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043331 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043331
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043331/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043331
Building REAL250005043332
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043332'
/scratch/stefan/7916125/working/building/REAL250005043332 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043332

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043332/0 /scratch/stefan/7916125/working/building/REAL250005043332 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/440
`/scratch/stefan/7916125/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043332 none O=C(CC1CC1)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 23, 23, 81, 81, 81, 163, 201, 201, 201, 201, 201, 201, 201, 201, 81, 3, 3, 1, 1, 1, 1, 1, 23, 81, 81, 81, 81, 163, 163, 201, 201, 81, 81] 201
rigid atoms, others: [2, 3, 4, 5, 23, 24, 25, 26, 27] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 743
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043332 none O=C(CC1CC1)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 51, 81, 81, 1, 1, 1, 1, 1, 7, 41, 41, 41, 50, 50, 50, 50, 50, 1, 51, 51, 81, 81, 81, 81, 81, 6, 1, 1, 1, 1, 7, 7, 41, 50, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 402
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043332 none O=C(CC1CC1)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [115, 115, 115, 177, 201, 201, 50, 50, 50, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 177, 177, 201, 201, 201, 201, 201, 115, 50, 50, 50, 50, 16, 16, 4, 1, 50, 50] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 757
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043332 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043332
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043332/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043332
Building REAL250005043333
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043333'
/scratch/stefan/7916125/working/building/REAL250005043333 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043333

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043333/0 /scratch/stefan/7916125/working/building/REAL250005043333 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/441
`/scratch/stefan/7916125/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043333 none CC(C)(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 6, 47, 47, 6, 6, 1, 1, 1, 1, 1, 9, 48, 48, 48, 80, 80, 80, 80, 80, 1, 47, 47, 47, 47, 47, 47, 6, 1, 1, 1, 1, 9, 9, 48, 80, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043333 none CC(C)(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 147, 201, 201, 147, 147, 80, 80, 80, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 147, 80, 80, 80, 80, 27, 27, 6, 1, 80, 80] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 713
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043333 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043333
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043333/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043333
Building REAL250005043334
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043334'
/scratch/stefan/7916125/working/building/REAL250005043334 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043334

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043334/0 /scratch/stefan/7916125/working/building/REAL250005043334 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/442
`/scratch/stefan/7916125/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043334 none COCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [94, 53, 6, 6, 6, 1, 1, 1, 1, 1, 7, 43, 43, 43, 58, 58, 58, 58, 58, 1, 94, 94, 94, 53, 53, 6, 1, 1, 1, 1, 7, 7, 43, 58, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 375
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043334 none COCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 136, 136, 136, 58, 58, 58, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 200, 200, 136, 58, 58, 58, 58, 18, 18, 4, 1, 58, 58] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043334 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043334
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043334/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043334
Building REAL250005043335
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043335'
/scratch/stefan/7916125/working/building/REAL250005043335 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043335

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043335/0 /scratch/stefan/7916125/working/building/REAL250005043335 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/443
`/scratch/stefan/7916125/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043335 none CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 6, 6, 6, 1, 1, 1, 1, 1, 7, 45, 45, 45, 58, 58, 58, 58, 58, 1, 74, 74, 74, 74, 74, 46, 46, 6, 1, 1, 1, 1, 7, 7, 45, 58, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 37, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 539
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043335 none CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 134, 134, 134, 58, 58, 58, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 197, 197, 134, 58, 58, 58, 58, 20, 20, 4, 1, 58, 58] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043335 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043335
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043335/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043335
Building REAL250005043336
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043336'
/scratch/stefan/7916125/working/building/REAL250005043336 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043336

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043336/0 /scratch/stefan/7916125/working/building/REAL250005043336 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/444
`/scratch/stefan/7916125/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043336 none CC(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 37, 6, 6, 6, 1, 1, 1, 1, 1, 9, 47, 47, 47, 67, 67, 67, 67, 67, 1, 37, 37, 37, 37, 37, 37, 37, 27, 27, 6, 1, 1, 1, 1, 9, 9, 47, 67, 1, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 346
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043336 none CC(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 116, 116, 116, 67, 67, 67, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 200, 200, 116, 67, 67, 67, 67, 25, 25, 5, 1, 67, 67] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 746
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043336 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043336
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043336/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043336
Building REAL250005043337
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043337'
/scratch/stefan/7916125/working/building/REAL250005043337 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043337

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043337/0 /scratch/stefan/7916125/working/building/REAL250005043337 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/445
`/scratch/stefan/7916125/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043337 none CC1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 48, 48, 48, 141, 201, 201, 201, 201, 201, 201, 201, 201, 48, 2, 2, 2, 1, 1, 1, 1, 13, 48, 48, 48, 48, 141, 141, 201, 201, 48, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 719
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043337 none CC1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 6, 6, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 81, 81, 81, 81, 81, 1, 48, 48, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 9, 9, 50, 81, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043337 none CC1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 144, 144, 144, 81, 81, 81, 27, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 144, 81, 81, 81, 81, 26, 26, 5, 1, 81, 81] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043337 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043337
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043337/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043337
Building REAL250005043338
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043338'
/scratch/stefan/7916125/working/building/REAL250005043338 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043338

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043338/0 /scratch/stefan/7916125/working/building/REAL250005043338 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/446
`/scratch/stefan/7916125/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043338 none CCOCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 71, 33, 6, 6, 6, 1, 1, 1, 1, 1, 7, 41, 41, 41, 65, 65, 65, 65, 65, 1, 75, 75, 75, 75, 75, 33, 33, 6, 1, 1, 1, 1, 7, 7, 41, 65, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 339
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043338 none CCOCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 133, 133, 133, 65, 65, 65, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 200, 200, 133, 65, 65, 65, 65, 23, 23, 4, 1, 65, 65] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043338 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043338
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043338/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043338
Building REAL250005043339
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043339'
/scratch/stefan/7916125/working/building/REAL250005043339 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043339

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043339/0 /scratch/stefan/7916125/working/building/REAL250005043339 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/447
`/scratch/stefan/7916125/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043339 none CC(C)=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 6, 6, 6, 1, 1, 1, 1, 1, 10, 53, 53, 53, 102, 102, 102, 102, 102, 1, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 1, 1, 10, 10, 53, 102, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 278
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043339 none CC(C)=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 164, 164, 164, 102, 102, 102, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 164, 102, 102, 102, 102, 36, 36, 7, 1, 102, 102] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 666
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043339 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043339
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043339/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043339
Building REAL250005043340
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043340'
/scratch/stefan/7916125/working/building/REAL250005043340 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043340

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043340/0 /scratch/stefan/7916125/working/building/REAL250005043340 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/448
`/scratch/stefan/7916125/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043340 none CSCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 45, 6, 6, 6, 1, 1, 1, 1, 1, 7, 36, 36, 36, 36, 36, 36, 36, 36, 1, 101, 101, 101, 45, 45, 6, 1, 1, 1, 1, 7, 7, 36, 36, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043340 none CSCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 183, 96, 96, 96, 36, 36, 36, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 183, 183, 96, 36, 36, 36, 36, 10, 10, 2, 1, 36, 36] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043340 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043340
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043340/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043340
Building REAL250005043341
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043341'
/scratch/stefan/7916125/working/building/REAL250005043341 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043341

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043341/0 /scratch/stefan/7916125/working/building/REAL250005043341 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/449
`/scratch/stefan/7916125/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043341 none CCCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 55, 45, 6, 6, 6, 1, 1, 1, 1, 1, 6, 37, 37, 37, 40, 40, 40, 40, 40, 1, 70, 70, 70, 70, 70, 69, 69, 45, 45, 6, 1, 1, 1, 1, 6, 6, 37, 40, 1, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 467
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043341 none CCCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 103, 103, 103, 40, 40, 40, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 194, 194, 103, 40, 40, 40, 40, 13, 13, 4, 1, 40, 40] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 766
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043341 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043341
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043341/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043341
Building REAL250005043342
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043342'
/scratch/stefan/7916125/working/building/REAL250005043342 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043342

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043342/0 /scratch/stefan/7916125/working/building/REAL250005043342 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/450
`/scratch/stefan/7916125/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043342 none CC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 42, 6, 6, 1, 1, 1, 1, 1, 9, 53, 53, 53, 108, 108, 108, 108, 108, 1, 42, 42, 42, 42, 42, 42, 42, 6, 1, 1, 1, 1, 9, 9, 53, 108, 1, 1] 201
rigid atoms, others: [36, 5, 6, 7, 8, 9, 37, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 353
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043342 none CC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 173, 173, 108, 108, 108, 39, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 201, 173, 108, 108, 108, 108, 39, 39, 7, 1, 108, 108] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 709
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043342 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043342
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043342/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043342
Building REAL250005043343
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043343'
/scratch/stefan/7916125/working/building/REAL250005043343 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043343

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043343/0 /scratch/stefan/7916125/working/building/REAL250005043343 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/451
`/scratch/stefan/7916125/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043343 none CCC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 32, 6, 32, 6, 6, 1, 1, 1, 1, 1, 7, 41, 41, 41, 55, 55, 55, 55, 55, 1, 50, 50, 50, 50, 50, 32, 32, 32, 32, 6, 1, 1, 1, 1, 7, 7, 41, 55, 1, 1] 201
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 356
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043343 none CCC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 122, 200, 122, 122, 55, 55, 55, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 200, 200, 200, 200, 122, 55, 55, 55, 55, 18, 18, 4, 1, 55, 55] 201
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043343 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043343
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043343/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043343
Building REAL250005043344
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043344'
/scratch/stefan/7916125/working/building/REAL250005043344 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043344

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043344/0 /scratch/stefan/7916125/working/building/REAL250005043344 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/452
`/scratch/stefan/7916125/working/3D/452' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043344 none COC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 51, 6, 51, 6, 6, 1, 1, 1, 1, 1, 7, 41, 41, 41, 61, 61, 61, 61, 61, 1, 73, 73, 73, 51, 51, 51, 51, 6, 1, 1, 1, 1, 7, 7, 41, 61, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 343
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043344 none COC(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 133, 201, 133, 133, 61, 61, 61, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 201, 133, 61, 61, 61, 61, 22, 22, 4, 1, 61, 61] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 745
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043344 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043344
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043344/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043344
Building REAL250005043345
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043345'
/scratch/stefan/7916125/working/building/REAL250005043345 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043345

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043345/0 /scratch/stefan/7916125/working/building/REAL250005043345 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/453
`/scratch/stefan/7916125/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043345 none C=CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 44, 43, 6, 6, 6, 1, 1, 1, 1, 1, 5, 32, 32, 32, 73, 73, 73, 73, 73, 1, 87, 87, 87, 44, 44, 43, 43, 6, 1, 1, 1, 1, 5, 5, 32, 73, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 435
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043345 none C=CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 73, 73, 73, 32, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 127, 73, 73, 73, 73, 32, 32, 6, 1, 73, 73] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 785
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043345 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043345
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043345/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043345
Building REAL250005043346
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043346'
/scratch/stefan/7916125/working/building/REAL250005043346 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043346

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043346/0 /scratch/stefan/7916125/working/building/REAL250005043346 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/454
`/scratch/stefan/7916125/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043346 none CC(C#N)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 56, 56, 6, 6, 1, 1, 1, 1, 1, 9, 49, 49, 49, 65, 65, 65, 65, 65, 1, 56, 56, 56, 56, 6, 1, 1, 1, 1, 9, 9, 49, 65, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 328
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043346 none CC(C#N)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 141, 201, 201, 141, 141, 65, 65, 65, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 141, 65, 65, 65, 65, 21, 21, 4, 1, 65, 65] 201
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 740
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043346 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043346
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043346/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043346
Building REAL250005043347
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043347'
/scratch/stefan/7916125/working/building/REAL250005043347 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043347

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043347/0 /scratch/stefan/7916125/working/building/REAL250005043347 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/455
`/scratch/stefan/7916125/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043347 none CC=C(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 43, 6, 43, 6, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 82, 82, 82, 82, 82, 1, 43, 43, 43, 43, 43, 43, 43, 6, 1, 1, 1, 1, 9, 9, 51, 82, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 279
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043347 none CC=C(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 201, 149, 149, 82, 82, 82, 31, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 149, 82, 82, 82, 82, 31, 31, 6, 1, 82, 82] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 677
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043347 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043347
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043347/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043347
Building REAL250005043348
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043348'
/scratch/stefan/7916125/working/building/REAL250005043348 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043348

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043348/0 /scratch/stefan/7916125/working/building/REAL250005043348 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/456
`/scratch/stefan/7916125/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043348 none CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 6, 6, 6, 1, 1, 1, 1, 1, 10, 57, 57, 57, 118, 118, 118, 118, 118, 1, 49, 49, 49, 49, 49, 6, 1, 1, 1, 1, 10, 10, 57, 118, 1, 1] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 399
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043348 none CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 168, 168, 168, 118, 118, 118, 42, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 168, 118, 118, 118, 118, 42, 42, 8, 1, 118, 118] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 733
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043348 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043348
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043348/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043348
Building REAL250005043349
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043349'
/scratch/stefan/7916125/working/building/REAL250005043349 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043349

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043349/0 /scratch/stefan/7916125/working/building/REAL250005043349 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/457
`/scratch/stefan/7916125/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043349 none COCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [77, 54, 39, 6, 6, 6, 1, 1, 1, 1, 1, 6, 34, 34, 34, 58, 58, 58, 58, 58, 1, 77, 77, 77, 54, 54, 39, 39, 6, 1, 1, 1, 1, 6, 6, 34, 58, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 385
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043349 none COCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 118, 118, 118, 58, 58, 58, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 191, 191, 118, 58, 58, 58, 58, 24, 24, 4, 1, 58, 58] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 763
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043349 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043349
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043349/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043349
Building REAL250005043350
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043350'
/scratch/stefan/7916125/working/building/REAL250005043350 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043350

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043350/0 /scratch/stefan/7916125/working/building/REAL250005043350 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/458
`/scratch/stefan/7916125/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043350 none CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 9, 39, 39, 39, 64, 64, 64, 64, 64, 1, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 39, 64, 1, 1] 69
rigid atoms, others: [3, 4, 5, 6, 7, 17, 22, 23, 24, 25, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 26, 27, 28, 29])
total number of confs: 158
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043350 none CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 64, 64, 64, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 64, 69, 69, 69, 69, 64, 64, 64, 64, 34, 34, 10, 1, 64, 64] 69
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31])
total number of confs: 239
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043350 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043350
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043350/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043350
Building REAL250005043351
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043351'
/scratch/stefan/7916125/working/building/REAL250005043351 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043351

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043351/0 /scratch/stefan/7916125/working/building/REAL250005043351 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/459
`/scratch/stefan/7916125/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043351 none O=C(NCC1CC(NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 1, 51, 75, 75, 75, 75, 75, 51, 9, 9, 1, 1, 1, 1, 6, 44, 44, 44, 44, 44, 1, 1, 75] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 13, 23, 24, 25, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 35])
total number of confs: 271
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043351 none O=C(NCC1CC(NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 43, 43, 43, 12, 12, 1, 12, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 139, 139, 43, 43, 43, 43, 12, 1, 1, 1, 1, 1, 43, 43, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 698
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: REAL250005043351 none O=C(NCC1CC(NC(=O)C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 22, 75, 75, 75, 126, 126, 126, 201, 201, 75, 1, 1, 1, 1, 1, 1, 4, 22, 22, 75, 75, 75, 75, 126, 201, 201, 201, 201, 201, 75, 75, 1] 201
rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 638
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043351 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043351
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043351/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043351
Building REAL250005043352
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043352'
/scratch/stefan/7916125/working/building/REAL250005043352 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043352

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043352/0 /scratch/stefan/7916125/working/building/REAL250005043352 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/460
`/scratch/stefan/7916125/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043352 none O=C(NCC1CC(NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 9, 1, 1, 1, 1, 1, 6, 6, 6, 39, 39, 39, 1, 50, 68, 68, 68, 68, 68, 50, 9, 9, 1, 1, 1, 1, 6, 39, 39, 39, 39, 39, 39, 39, 1, 1, 68] 201
rigid atoms, others: [3, 4, 5, 6, 7, 14, 24, 25, 26, 27, 37, 36] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 38])
total number of confs: 248
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043352 none O=C(NCC1CC(NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 39, 39, 39, 11, 11, 1, 11, 1, 1, 1, 1, 39, 201, 201, 201, 201, 201, 201, 201, 132, 132, 39, 39, 39, 39, 11, 1, 1, 1, 1, 1, 1, 1, 39, 39, 201] 201
rigid atoms, others: [32, 33, 34, 35, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38])
total number of confs: 700
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: REAL250005043352 none O=C(NCC1CC(NC(=O)C2CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 20, 68, 68, 68, 124, 124, 124, 201, 201, 201, 68, 1, 1, 1, 1, 1, 1, 3, 20, 20, 68, 68, 68, 68, 124, 201, 201, 201, 201, 201, 201, 201, 68, 68, 1] 201
rigid atoms, others: [1, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 621
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043352 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043352
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043352/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043352
Building REAL250005043353
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043353'
/scratch/stefan/7916125/working/building/REAL250005043353 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043353

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043353/0 /scratch/stefan/7916125/working/building/REAL250005043353 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/461
`/scratch/stefan/7916125/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043353 none NC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
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: [30, 6, 36, 6, 6, 1, 1, 1, 1, 1, 9, 49, 49, 49, 72, 72, 72, 72, 72, 1, 30, 36, 6, 1, 1, 1, 1, 9, 9, 49, 72, 1, 1] 133
rigid atoms, others: [32, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 251
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043353 none NC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 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]
0  hydrogens need rotated
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [132, 124, 133, 124, 124, 72, 72, 72, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 72, 132, 133, 124, 72, 72, 72, 72, 23, 23, 6, 1, 72, 72] 133
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 414
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043353 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043353
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043353/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043353
Building REAL250005043354
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043354'
/scratch/stefan/7916125/working/building/REAL250005043354 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043354

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043354/0 /scratch/stefan/7916125/working/building/REAL250005043354 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/462
`/scratch/stefan/7916125/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043354 none CC(C)(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 1, 10, 48, 48, 48, 82, 82, 82, 82, 82, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 10, 10, 48, 82, 1, 1] 111
rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 234
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043354 none CC(C)(C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 109, 111, 111, 109, 109, 82, 82, 82, 33, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 82, 111, 111, 111, 111, 111, 111, 111, 111, 111, 109, 82, 82, 82, 82, 32, 32, 9, 1, 82, 82] 111
rigid atoms, others: [38, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 364
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043354 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043354
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043354/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043354
Building REAL250005043355
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043355'
/scratch/stefan/7916125/working/building/REAL250005043355 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043355

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043355/0 /scratch/stefan/7916125/working/building/REAL250005043355 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/463
`/scratch/stefan/7916125/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2CC(CNC(=O)C3=CC(=O)[N-]O3)C2)CC1)

`REAL250005043355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043355 none CC1(C(=O)NC2CC(CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 30, 30, 30, 123, 201, 201, 201, 201, 201, 201, 201, 201, 30, 1, 1, 2, 2, 2, 7, 30, 30, 30, 30, 123, 123, 201, 201, 30, 30, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 722
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043355 none CC1(C(=O)NC2CC(CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 6, 6, 6, 1, 1, 1, 1, 1, 9, 46, 46, 46, 78, 78, 78, 78, 78, 1, 30, 30, 30, 30, 30, 6, 1, 1, 1, 1, 9, 9, 46, 78, 1, 1, 30, 30, 30, 30] 201
rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 18, 25, 26, 27, 28] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 243
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043355 none CC1(C(=O)NC2CC(CNC(=O)C3=CC(=O)[N-]O3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 78, 78, 78, 27, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 122, 78, 78, 78, 78, 26, 26, 5, 1, 78, 78, 201, 201, 201, 201] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 638
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043355 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043355
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043355/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043355
Building REAL250005043356
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043356'
/scratch/stefan/7916125/working/building/REAL250005043356 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043356

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043356/0 /scratch/stefan/7916125/working/building/REAL250005043356 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/464
`/scratch/stefan/7916125/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043356 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 48, 48, 141, 201, 201, 201, 201, 201, 201, 201, 201, 48, 2, 2, 2, 1, 1, 13, 48, 48, 48, 48, 141, 141, 201, 201, 48, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 719
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043356 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 6, 48, 6, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 81, 81, 81, 81, 81, 1, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 9, 9, 50, 81, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043356 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 143, 201, 143, 143, 81, 81, 81, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 143, 81, 81, 81, 81, 26, 26, 5, 1, 81, 81] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043356 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043356
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043356/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043356
Building REAL250005043357
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043357'
/scratch/stefan/7916125/working/building/REAL250005043357 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043357

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043357/0 /scratch/stefan/7916125/working/building/REAL250005043357 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/465
`/scratch/stefan/7916125/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043357 none CCC(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 38, 6, 38, 6, 6, 1, 1, 1, 1, 1, 9, 44, 44, 44, 54, 54, 54, 54, 54, 1, 62, 62, 62, 62, 62, 38, 6, 1, 1, 1, 1, 9, 9, 44, 54, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 433
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043357 none CCC(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 182, 133, 182, 133, 133, 54, 54, 54, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 182, 133, 54, 54, 54, 54, 18, 18, 4, 1, 54, 54] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 746
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043357 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043357
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043357/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043357
Building REAL250005043358
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043358'
/scratch/stefan/7916125/working/building/REAL250005043358 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043358

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043358/0 /scratch/stefan/7916125/working/building/REAL250005043358 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/466
`/scratch/stefan/7916125/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043358 none O=C(CCCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 41, 53, 91, 1, 1, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28, 28, 1, 41, 41, 67, 67, 85, 86, 6, 1, 1, 1, 1, 6, 6, 28, 28, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 533
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043358 none O=C(CCCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 184, 193, 201, 28, 28, 28, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 184, 184, 201, 201, 201, 201, 71, 28, 28, 28, 28, 9, 9, 2, 1, 28, 28] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 834
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043358 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043358
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043358/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043358
Building REAL250005043359
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043359'
/scratch/stefan/7916125/working/building/REAL250005043359 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043359

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043359/0 /scratch/stefan/7916125/working/building/REAL250005043359 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/467
`/scratch/stefan/7916125/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043359 none C[C@H]1C[C@@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 44, 44, 44, 146, 201, 201, 201, 201, 201, 201, 201, 201, 44, 2, 2, 2, 1, 1, 12, 44, 44, 44, 44, 146, 146, 201, 201, 44, 44] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 719
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043359 none C[C@H]1C[C@@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 44, 44, 44, 6, 44, 6, 6, 1, 1, 1, 1, 1, 9, 48, 48, 48, 64, 64, 64, 64, 64, 1, 44, 44, 44, 44, 44, 6, 1, 1, 1, 1, 9, 9, 48, 64, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 252
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: REAL250005043359 none C[C@H]1C[C@@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 128, 201, 128, 128, 64, 64, 64, 18, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 128, 64, 64, 64, 64, 18, 18, 3, 1, 64, 64] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 625
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043359 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043359
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043359/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043359
Building REAL250005043360
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043360'
/scratch/stefan/7916125/working/building/REAL250005043360 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043360

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043360/0 /scratch/stefan/7916125/working/building/REAL250005043360 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/468
`/scratch/stefan/7916125/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043360 none O=C(CO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
354  conformations in input
total number of sets (complete confs): 354
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 49, 1, 1, 1, 1, 1, 9, 47, 47, 47, 68, 68, 68, 68, 68, 1, 49, 49, 147, 6, 1, 1, 1, 1, 9, 9, 47, 68, 1, 1] 354
rigid atoms, others: [32, 4, 5, 6, 7, 8, 18, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 461
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043360 none O=C(CO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 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]
1  hydrogens need rotated
354  conformations in input
total number of sets (complete confs): 354
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 118, 68, 68, 68, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 68, 118, 118, 354, 114, 68, 68, 68, 68, 23, 23, 6, 1, 68, 68] 354
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043360 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043360
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043360/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043360
Building REAL250005043361
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043361'
/scratch/stefan/7916125/working/building/REAL250005043361 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043361

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043361/0 /scratch/stefan/7916125/working/building/REAL250005043361 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/469
`/scratch/stefan/7916125/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1)

`REAL250005043361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043361 none O=C(NCC1CC(NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 10, 1, 1, 1, 1, 1, 6, 6, 6, 44, 44, 44, 1, 61, 103, 103, 103, 103, 103, 61, 10, 10, 1, 1, 1, 1, 6, 44, 44, 44, 44, 44, 1, 1, 103] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 14, 35, 24, 25, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 322
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043361 none O=C(NCC1CC(NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 198, 138, 44, 44, 44, 11, 11, 1, 11, 1, 1, 1, 1, 44, 198, 201, 201, 201, 201, 201, 198, 138, 138, 44, 44, 44, 44, 11, 1, 1, 1, 1, 1, 44, 44, 201] 201
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 701
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: REAL250005043361 none O=C(NCC1CC(NC(=O)C2CCO2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 34, 103, 103, 103, 174, 174, 174, 201, 201, 201, 103, 1, 1, 1, 1, 1, 1, 6, 34, 34, 103, 103, 103, 103, 174, 201, 201, 201, 201, 201, 103, 103, 1] 201
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 631
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043361 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043361
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043361/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043361
Building REAL250005043362
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043362'
/scratch/stefan/7916125/working/building/REAL250005043362 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043362

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043362/0 /scratch/stefan/7916125/working/building/REAL250005043362 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/470
`/scratch/stefan/7916125/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043362 none O=C(NCC1CC(NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 9, 1, 1, 1, 1, 1, 6, 6, 6, 42, 42, 42, 1, 50, 66, 66, 66, 66, 66, 50, 9, 9, 1, 1, 1, 1, 6, 42, 42, 42, 42, 42, 1, 1, 66] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 14, 35, 24, 25, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 251
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043362 none O=C(NCC1CC(NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 42, 42, 42, 11, 11, 1, 11, 1, 1, 1, 1, 42, 201, 201, 201, 201, 201, 201, 201, 139, 139, 42, 42, 42, 42, 11, 1, 1, 1, 1, 1, 42, 42, 201] 201
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 724
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: REAL250005043362 none O=C(NCC1CC(NC(=O)C2COC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 20, 66, 66, 66, 138, 138, 138, 201, 201, 201, 66, 1, 1, 1, 1, 1, 1, 4, 20, 20, 66, 66, 66, 66, 138, 201, 201, 201, 201, 201, 66, 66, 1] 201
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 624
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043362 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043362
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043362/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043362
Building REAL250005043363
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043363'
/scratch/stefan/7916125/working/building/REAL250005043363 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043363

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043363/0 /scratch/stefan/7916125/working/building/REAL250005043363 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/471
`/scratch/stefan/7916125/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043363 none O=C(C=CCO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 27, 27, 73, 1, 1, 1, 1, 1, 6, 37, 37, 37, 84, 84, 84, 84, 84, 1, 27, 27, 73, 73, 219, 6, 1, 1, 1, 1, 6, 6, 37, 84, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 639
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043363 none O=C(C=CCO)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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, 1, 1, 5, 12, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [155, 155, 155, 201, 201, 201, 84, 84, 84, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 603, 155, 84, 84, 84, 84, 35, 35, 7, 1, 84, 84] 603
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1268
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043363 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043363
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043363/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043363
Building REAL250005043364
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043364'
/scratch/stefan/7916125/working/building/REAL250005043364 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043364

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043364/0 /scratch/stefan/7916125/working/building/REAL250005043364 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/472
`/scratch/stefan/7916125/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043364 none CCC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 36, 36, 6, 6, 6, 1, 1, 1, 1, 1, 7, 40, 40, 40, 57, 57, 57, 57, 57, 1, 70, 70, 70, 70, 70, 36, 36, 6, 1, 1, 1, 1, 7, 7, 40, 57, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 401
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043364 none CCC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 122, 122, 122, 57, 57, 57, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 164, 164, 122, 57, 57, 57, 57, 22, 22, 4, 1, 57, 57] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 756
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043364 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043364
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043364/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043364
Building REAL250005043365
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043365'
/scratch/stefan/7916125/working/building/REAL250005043365 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043365

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043365/0 /scratch/stefan/7916125/working/building/REAL250005043365 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/473
`/scratch/stefan/7916125/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043365 none C#CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 43, 6, 6, 6, 1, 1, 1, 1, 1, 7, 39, 39, 39, 44, 44, 44, 44, 44, 1, 67, 67, 67, 43, 43, 6, 1, 1, 1, 1, 7, 7, 39, 44, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 381
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043365 none C#CCCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 181, 107, 107, 107, 44, 44, 44, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 181, 181, 107, 44, 44, 44, 44, 14, 14, 3, 1, 44, 44] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 764
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043365 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043365
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043365/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043365
Building REAL250005043366
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043366'
/scratch/stefan/7916125/working/building/REAL250005043366 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043366

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043366/0 /scratch/stefan/7916125/working/building/REAL250005043366 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/474
`/scratch/stefan/7916125/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043366 none C=CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [98, 52, 6, 52, 6, 6, 1, 1, 1, 1, 1, 7, 42, 42, 42, 50, 50, 50, 50, 50, 1, 98, 98, 98, 52, 156, 6, 1, 1, 1, 1, 7, 7, 42, 50, 1, 1] 603
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 584
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043366 none C=CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 200, 118, 201, 118, 118, 50, 50, 50, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 603, 118, 50, 50, 50, 50, 15, 15, 4, 1, 50, 50] 603
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 1365
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043366 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043366
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043366/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043366
Building REAL250005043367
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043367'
/scratch/stefan/7916125/working/building/REAL250005043367 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043367

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043367/0 /scratch/stefan/7916125/working/building/REAL250005043367 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/475
`/scratch/stefan/7916125/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043367 none CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
546  conformations in input
total number of sets (complete confs): 546
using faster count positions algorithm for large data
unique positions, atoms: [50, 6, 50, 6, 6, 1, 1, 1, 1, 1, 9, 48, 48, 48, 83, 83, 83, 83, 83, 1, 50, 50, 50, 50, 150, 6, 1, 1, 1, 1, 9, 9, 48, 83, 1, 1] 546
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043367 none CC(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
546  conformations in input
total number of sets (complete confs): 546
using faster count positions algorithm for large data
unique positions, atoms: [182, 149, 182, 149, 149, 83, 83, 83, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 182, 182, 182, 182, 546, 149, 83, 83, 83, 83, 32, 32, 7, 1, 83, 83] 546
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1204
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043367 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043367
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043367/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043367
Building REAL250005043368
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043368'
/scratch/stefan/7916125/working/building/REAL250005043368 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043368

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043368/0 /scratch/stefan/7916125/working/building/REAL250005043368 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/476
`/scratch/stefan/7916125/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043368 none CC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [35, 6, 35, 6, 6, 1, 1, 1, 1, 1, 9, 49, 49, 49, 75, 75, 75, 75, 75, 1, 35, 35, 35, 6, 1, 1, 1, 1, 9, 9, 49, 75, 1, 1] 152
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 19, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 28, 29, 30, 31])
total number of confs: 252
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043368 none CC(=O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 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
152  conformations in input
total number of sets (complete confs): 152
using faster count positions algorithm for large data
unique positions, atoms: [152, 130, 152, 130, 130, 75, 75, 75, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 75, 152, 152, 152, 130, 75, 75, 75, 75, 27, 27, 6, 1, 75, 75] 152
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 485
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043368 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043368
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043368/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043368
Building REAL250005043369
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043369'
/scratch/stefan/7916125/working/building/REAL250005043369 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043369

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043369/0 /scratch/stefan/7916125/working/building/REAL250005043369 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/477
`/scratch/stefan/7916125/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043369 none O=C(NCC1CC(NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 53, 9, 1, 1, 1, 1, 1, 6, 6, 6, 43, 43, 43, 1, 53, 73, 73, 73, 73, 73, 53, 9, 9, 1, 1, 1, 1, 6, 43, 43, 43, 43, 1, 1, 73] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 14, 24, 25, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 35])
total number of confs: 265
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043369 none O=C(NCC1CC(NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 144, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 144, 144, 43, 43, 43, 43, 11, 1, 1, 1, 1, 43, 43, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 716
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: REAL250005043369 none O=C(NCC1CC(NC(=O)C2(F)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 22, 73, 73, 73, 164, 164, 164, 201, 201, 201, 73, 1, 1, 1, 1, 1, 1, 3, 21, 21, 73, 73, 73, 73, 164, 201, 201, 201, 201, 73, 73, 1] 201
rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 605
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043369 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043369
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043369/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043369
Building REAL250005043370
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043370'
/scratch/stefan/7916125/working/building/REAL250005043370 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043370

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043370/0 /scratch/stefan/7916125/working/building/REAL250005043370 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/478
`/scratch/stefan/7916125/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043370 none CC=C(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 6, 48, 6, 6, 1, 1, 1, 1, 1, 10, 53, 53, 53, 93, 93, 93, 93, 93, 1, 50, 50, 50, 50, 6, 1, 1, 1, 1, 10, 10, 53, 93, 1, 1] 189
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 310
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043370 none CC=C(F)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
189  conformations in input
total number of sets (complete confs): 189
using faster count positions algorithm for large data
unique positions, atoms: [189, 189, 162, 189, 162, 162, 93, 93, 93, 36, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 93, 189, 189, 189, 189, 162, 93, 93, 93, 93, 36, 36, 8, 1, 93, 93] 189
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 597
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043370 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043370
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043370/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043370
Building REAL250005043371
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043371'
/scratch/stefan/7916125/working/building/REAL250005043371 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043371

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043371/0 /scratch/stefan/7916125/working/building/REAL250005043371 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/479
`/scratch/stefan/7916125/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043371 none CC(CO)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 74, 6, 6, 1, 1, 1, 1, 1, 7, 43, 43, 43, 51, 51, 51, 51, 51, 1, 36, 36, 36, 36, 74, 74, 222, 6, 1, 1, 1, 1, 7, 7, 43, 51, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 638
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043371 none CC(CO)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [193, 116, 193, 201, 116, 116, 51, 51, 51, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 51, 193, 193, 193, 193, 201, 201, 603, 116, 51, 51, 51, 51, 14, 14, 3, 1, 51, 51] 603
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1358
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043371 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043371
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043371/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043371
Building REAL250005043372
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043372'
/scratch/stefan/7916125/working/building/REAL250005043372 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043372

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043372/0 /scratch/stefan/7916125/working/building/REAL250005043372 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/480
`/scratch/stefan/7916125/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1)

`REAL250005043372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043372 none O=C(NCC1CC(NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [53, 53, 9, 1, 1, 1, 1, 1, 6, 6, 6, 43, 43, 43, 1, 53, 77, 77, 77, 77, 77, 53, 9, 9, 1, 1, 1, 1, 6, 129, 43, 43, 43, 43, 1, 1, 77] 603
rigid atoms, others: [34, 3, 4, 5, 6, 7, 14, 35, 24, 25, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 36])
total number of confs: 402
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043372 none O=C(NCC1CC(NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 142, 43, 43, 43, 11, 11, 1, 11, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 142, 142, 43, 43, 43, 43, 11, 6, 1, 1, 1, 1, 43, 43, 201] 603
rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36])
total number of confs: 722
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: REAL250005043372 none O=C(NCC1CC(NC(=O)C2(O)CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 4, 24, 77, 77, 77, 179, 179, 179, 201, 201, 201, 77, 1, 1, 1, 1, 1, 1, 4, 24, 24, 77, 77, 77, 77, 179, 603, 201, 201, 201, 201, 77, 77, 1] 603
rigid atoms, others: [1, 36, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 1207
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043372 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043372
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043372/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043372
Building REAL250005043373
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043373'
/scratch/stefan/7916125/working/building/REAL250005043373 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043373

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043373/0 /scratch/stefan/7916125/working/building/REAL250005043373 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/481
`/scratch/stefan/7916125/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1)

`REAL250005043373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043373 none O=C(NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 10, 47, 47, 47, 71, 71, 71, 71, 71, 1, 6, 19, 19, 19, 6, 1, 1, 1, 1, 10, 10, 47, 71, 1, 1, 19, 19, 19, 19, 19] 90
rigid atoms, others: [2, 3, 4, 5, 6, 16, 22, 23, 24, 25, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 26, 27, 28, 29, 32, 33, 34, 35, 36])
total number of confs: 192
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043373 none O=C(NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 71, 71, 71, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 90, 90, 90, 90, 90, 71, 71, 71, 71, 30, 30, 8, 1, 71, 71, 90, 90, 90, 90, 90] 90
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 295
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: REAL250005043373 none O=C(NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)C1=CCC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 10, 10, 19, 19, 19, 54, 81, 81, 81, 90, 90, 90, 90, 90, 19, 1, 1, 1, 1, 10, 19, 19, 19, 19, 54, 54, 81, 90, 19, 19, 1, 1, 1, 1, 1] 90
rigid atoms, others: [32, 1, 34, 35, 36, 33, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 306
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043373 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043373
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043373/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043373
Building REAL250005043374
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043374'
/scratch/stefan/7916125/working/building/REAL250005043374 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043374

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043374/0 /scratch/stefan/7916125/working/building/REAL250005043374 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/482
`/scratch/stefan/7916125/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043374 none CC(CF)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 6, 38, 90, 6, 6, 1, 1, 1, 1, 1, 7, 38, 38, 38, 44, 44, 44, 44, 44, 1, 38, 38, 38, 38, 90, 90, 6, 1, 1, 1, 1, 7, 7, 38, 44, 1, 1] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043374 none CC(CF)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 109, 198, 201, 109, 109, 44, 44, 44, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 198, 198, 198, 198, 201, 201, 109, 44, 44, 44, 44, 14, 14, 4, 1, 44, 44] 201
rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 742
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043374 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043374
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043374/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043374
Building REAL250005043375
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043375'
/scratch/stefan/7916125/working/building/REAL250005043375 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043375

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043375/0 /scratch/stefan/7916125/working/building/REAL250005043375 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/483
`/scratch/stefan/7916125/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043375 none CC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [39, 39, 6, 6, 6, 1, 1, 1, 1, 1, 10, 54, 54, 54, 108, 108, 108, 108, 108, 1, 39, 39, 39, 39, 39, 6, 1, 1, 1, 1, 10, 10, 54, 108, 1, 1] 167
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 311
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043375 none CC=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 167, 139, 139, 139, 108, 108, 108, 40, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 108, 167, 167, 167, 167, 167, 139, 108, 108, 108, 108, 40, 40, 7, 1, 108, 108] 167
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 560
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043375 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043375
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043375/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043375
Building REAL250005043376
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043376'
/scratch/stefan/7916125/working/building/REAL250005043376 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043376

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043376/0 /scratch/stefan/7916125/working/building/REAL250005043376 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/484
`/scratch/stefan/7916125/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043376 none O=C(C=CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 40, 40, 108, 1, 1, 1, 1, 1, 7, 42, 42, 42, 49, 49, 49, 49, 49, 1, 40, 40, 108, 108, 6, 1, 1, 1, 1, 7, 7, 42, 49, 1, 1] 201
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 489
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043376 none O=C(C=CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 197, 197, 201, 49, 49, 49, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 49, 197, 197, 201, 201, 125, 49, 49, 49, 49, 16, 16, 4, 1, 49, 49] 201
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 636
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043376 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043376
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043376/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043376
Building REAL250005043377
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043377'
/scratch/stefan/7916125/working/building/REAL250005043377 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005043377 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005043377' -> `/scratch/stefan/7916125/failed/REAL250005043377'
Building REAL250005043378
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043378'
/scratch/stefan/7916125/working/building/REAL250005043378 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043378

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043378/0 /scratch/stefan/7916125/working/building/REAL250005043378 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/485
`/scratch/stefan/7916125/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043378 none C[C@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
543  conformations in input
total number of sets (complete confs): 543
using faster count positions algorithm for large data
unique positions, atoms: [52, 6, 52, 52, 6, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 84, 84, 84, 84, 84, 1, 52, 52, 52, 156, 6, 1, 1, 1, 1, 9, 9, 50, 84, 1, 1] 543
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 505
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043378 none C[C@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
543  conformations in input
total number of sets (complete confs): 543
using faster count positions algorithm for large data
unique positions, atoms: [181, 152, 181, 181, 152, 152, 84, 84, 84, 32, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 84, 181, 181, 181, 543, 152, 84, 84, 84, 84, 32, 32, 6, 1, 84, 84] 543
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1177
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043378 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043378
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043378/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043378
Building REAL250005043379
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043379'
/scratch/stefan/7916125/working/building/REAL250005043379 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043379

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043379/0 /scratch/stefan/7916125/working/building/REAL250005043379 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/486
`/scratch/stefan/7916125/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043379 none CON=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [49, 26, 26, 6, 6, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 99, 99, 99, 99, 99, 1, 49, 49, 49, 26, 6, 1, 1, 1, 1, 9, 9, 51, 99, 1, 1] 154
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 305
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043379 none CON=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [154, 154, 154, 145, 145, 145, 99, 99, 99, 43, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 99, 154, 154, 154, 154, 145, 99, 99, 99, 99, 43, 43, 9, 1, 99, 99] 154
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 497
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043379 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043379
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043379/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043379
Building REAL250005043380
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043380'
/scratch/stefan/7916125/working/building/REAL250005043380 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043380

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043380/0 /scratch/stefan/7916125/working/building/REAL250005043380 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/487
`/scratch/stefan/7916125/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043380 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 48, 48, 48, 141, 201, 201, 201, 201, 201, 201, 201, 201, 48, 2, 2, 2, 1, 1, 13, 48, 48, 48, 48, 141, 141, 201, 201, 48, 48] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 719
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043380 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 48, 48, 48, 6, 48, 6, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 81, 81, 81, 81, 81, 1, 48, 48, 48, 48, 48, 6, 1, 1, 1, 1, 9, 9, 50, 81, 1, 1] 201
rigid atoms, others: [32, 37, 38, 8, 9, 10, 11, 12, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 286
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043380 none C[C@@H]1C[C@H]1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)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.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 143, 201, 143, 143, 81, 81, 81, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 143, 81, 81, 81, 81, 26, 26, 5, 1, 81, 81] 201
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043380 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043380
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043380/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043380
Building REAL250005043381
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043381'
/scratch/stefan/7916125/working/building/REAL250005043381 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043381

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043381/0 /scratch/stefan/7916125/working/building/REAL250005043381 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/488
`/scratch/stefan/7916125/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043381 none CC(C)(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [44, 6, 44, 44, 6, 6, 1, 1, 1, 1, 1, 9, 52, 52, 52, 89, 89, 89, 89, 89, 1, 44, 44, 44, 44, 44, 44, 132, 6, 1, 1, 1, 1, 9, 9, 52, 89, 1, 1] 603
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043381 none CC(C)(O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 150, 201, 201, 150, 150, 89, 89, 89, 30, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 603, 150, 89, 89, 89, 89, 30, 30, 6, 1, 89, 89] 603
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 1329
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043381 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043381
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043381/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043381
Building REAL250005043382
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043382'
/scratch/stefan/7916125/working/building/REAL250005043382 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043382

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043382/0 /scratch/stefan/7916125/working/building/REAL250005043382 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/489
`/scratch/stefan/7916125/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043382 none C=C(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 46, 84, 6, 6, 6, 1, 1, 1, 1, 1, 7, 38, 38, 38, 47, 47, 47, 47, 47, 1, 84, 84, 84, 84, 84, 46, 46, 6, 1, 1, 1, 1, 7, 7, 38, 47, 1, 1] 201
rigid atoms, others: [32, 37, 6, 7, 8, 9, 10, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 393
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043382 none C=C(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 113, 113, 113, 47, 47, 47, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 113, 47, 47, 47, 47, 19, 19, 4, 1, 47, 47] 201
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043382 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043382
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043382/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043382
Building REAL250005043383
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043383'
/scratch/stefan/7916125/working/building/REAL250005043383 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043383

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043383/0 /scratch/stefan/7916125/working/building/REAL250005043383 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/490
`/scratch/stefan/7916125/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043383 none C=CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [113, 56, 6, 6, 6, 1, 1, 1, 1, 1, 7, 39, 39, 39, 55, 55, 55, 55, 55, 1, 113, 113, 113, 56, 56, 6, 1, 1, 1, 1, 7, 7, 39, 55, 1, 1] 201
rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 19, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 477
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043383 none C=CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 127, 127, 127, 55, 55, 55, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 127, 55, 55, 55, 55, 20, 20, 4, 1, 55, 55] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 748
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043383 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043383
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043383/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043383
Building REAL250005043384
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043384'
/scratch/stefan/7916125/working/building/REAL250005043384 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043384

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043384/0 /scratch/stefan/7916125/working/building/REAL250005043384 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/491
`/scratch/stefan/7916125/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043384 none C[NH+](C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [38, 36, 38, 38, 6, 6, 6, 1, 1, 1, 1, 1, 7, 38, 38, 38, 64, 64, 64, 64, 64, 1, 38, 38, 38, 38, 38, 38, 36, 36, 6, 1, 1, 1, 1, 7, 7, 38, 64, 1, 1] 145
rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 40, 21, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043384 none C[NH+](C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 145, 145, 122, 122, 122, 64, 64, 64, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 64, 145, 145, 145, 145, 145, 145, 145, 145, 122, 64, 64, 64, 64, 28, 28, 8, 1, 64, 64] 145
rigid atoms, others: [38, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 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: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043384 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043384/1 /scratch/stefan/7916125/working/building/REAL250005043384 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/492
`/scratch/stefan/7916125/working/3D/492' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043384.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043384/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043384 none CN(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 6, 6, 6, 1, 1, 1, 1, 1, 7, 45, 45, 45, 57, 57, 57, 57, 57, 1, 68, 68, 68, 68, 68, 68, 40, 40, 6, 1, 1, 1, 1, 7, 7, 45, 57, 1, 1] 201
rigid atoms, others: [32, 33, 38, 6, 7, 8, 9, 10, 39, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043384 none CN(C)CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 121, 121, 121, 57, 57, 57, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 198, 198, 121, 57, 57, 57, 57, 18, 18, 4, 1, 57, 57] 201
rigid atoms, others: [37, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 726
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043384 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043384
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043384/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043384/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043384
Building REAL250005043385
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043385'
/scratch/stefan/7916125/working/building/REAL250005043385 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043385

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043385/0 /scratch/stefan/7916125/working/building/REAL250005043385 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/493
`/scratch/stefan/7916125/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043385 none N#CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 6, 6, 6, 1, 1, 1, 1, 1, 9, 51, 51, 51, 81, 81, 81, 81, 81, 1, 56, 56, 6, 1, 1, 1, 1, 9, 9, 51, 81, 1, 1] 201
rigid atoms, others: [32, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043385 none N#CCC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 154, 154, 154, 81, 81, 81, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 81, 201, 201, 154, 81, 81, 81, 81, 27, 27, 6, 1, 81, 81] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043385 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043385
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043385/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043385
Building REAL250005043386
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043386'
/scratch/stefan/7916125/working/building/REAL250005043386 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043386

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043386/0 /scratch/stefan/7916125/working/building/REAL250005043386 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/494
`/scratch/stefan/7916125/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(NCC1CC(NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1)

`REAL250005043386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043386 none O=C(NCC1CC(NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 50, 9, 1, 1, 1, 1, 1, 6, 6, 6, 47, 47, 47, 1, 50, 87, 87, 87, 87, 87, 50, 9, 9, 1, 1, 1, 1, 6, 47, 47, 47, 47, 1, 1, 87] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 14, 24, 25, 26, 27] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 35])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043386 none O=C(NCC1CC(NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 140, 47, 47, 47, 12, 12, 1, 12, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 140, 140, 47, 47, 47, 47, 12, 1, 1, 1, 1, 47, 47, 201] 201
rigid atoms, others: [32, 8, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35])
total number of confs: 718
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043386 none O=C(NCC1CC(NC(=O)C2CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 28, 87, 87, 87, 152, 152, 152, 201, 201, 201, 87, 1, 1, 1, 1, 1, 1, 6, 28, 28, 87, 87, 87, 87, 152, 201, 201, 201, 201, 87, 87, 1] 201
rigid atoms, others: [1, 35, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 628
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043386 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043386
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043386/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043386
Building REAL250005043387
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043387'
/scratch/stefan/7916125/working/building/REAL250005043387 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043387

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043387/0 /scratch/stefan/7916125/working/building/REAL250005043387 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/495
`/scratch/stefan/7916125/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043387 none O=C(CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 44, 87, 1, 1, 1, 1, 1, 7, 43, 43, 43, 54, 54, 54, 54, 54, 1, 44, 44, 87, 87, 6, 1, 1, 1, 1, 7, 7, 43, 54, 1, 1] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 506
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043387 none O=C(CCF)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 201, 201, 54, 54, 54, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 119, 54, 54, 54, 54, 19, 19, 4, 1, 54, 54] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 737
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043387 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043387
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043387/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043387
Building REAL250005043388
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043388'
/scratch/stefan/7916125/working/building/REAL250005043388 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043388

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043388/0 /scratch/stefan/7916125/working/building/REAL250005043388 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/496
`/scratch/stefan/7916125/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043388 none CO[C@H](C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 47, 6, 47, 47, 6, 6, 1, 1, 1, 1, 1, 7, 41, 41, 41, 59, 59, 59, 59, 59, 1, 71, 71, 71, 47, 47, 47, 6, 1, 1, 1, 1, 7, 7, 41, 59, 1, 1] 201
rigid atoms, others: [32, 37, 38, 7, 8, 9, 10, 11, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 330
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043388 none CO[C@H](C)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 132, 200, 200, 132, 132, 59, 59, 59, 21, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 200, 200, 200, 132, 59, 59, 59, 59, 20, 20, 3, 1, 59, 59] 201
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 749
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043388 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043388
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043388/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043388
Building REAL250005043389
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043389'
/scratch/stefan/7916125/working/building/REAL250005043389 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043389

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043389/0 /scratch/stefan/7916125/working/building/REAL250005043389 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/497
`/scratch/stefan/7916125/working/3D/497' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043389 none C[C@@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [48, 6, 48, 48, 6, 6, 1, 1, 1, 1, 1, 10, 56, 56, 56, 91, 91, 91, 91, 91, 1, 48, 48, 48, 144, 6, 1, 1, 1, 1, 10, 10, 56, 91, 1, 1] 603
rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 20, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 503
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043389 none C[C@@H](O)C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 170, 201, 201, 170, 170, 91, 91, 91, 27, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 603, 170, 91, 91, 91, 91, 26, 26, 5, 1, 91, 91] 603
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 1285
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043389 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043389
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043389/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043389
Building REAL250005043390
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043390'
/scratch/stefan/7916125/working/building/REAL250005043390 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043390

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043390/0 /scratch/stefan/7916125/working/building/REAL250005043390 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/498
`/scratch/stefan/7916125/working/3D/498' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043390 none C=C1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 52, 52, 52, 149, 201, 201, 201, 201, 201, 201, 201, 201, 52, 1, 1, 1, 1, 1, 13, 52, 52, 52, 52, 149, 149, 201, 201, 52, 52] 201
rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([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])
total number of confs: 737
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043390 none C=C1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 6, 6, 6, 1, 1, 1, 1, 1, 9, 50, 50, 50, 74, 74, 74, 74, 74, 1, 52, 52, 52, 52, 52, 6, 1, 1, 1, 1, 9, 9, 50, 74, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
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: REAL250005043390 none C=C1CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 143, 143, 143, 74, 74, 74, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 143, 74, 74, 74, 74, 25, 25, 5, 1, 74, 74] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 624
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043390 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043390
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043390/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043390
Building REAL250005043391
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043391'
/scratch/stefan/7916125/working/building/REAL250005043391 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043391

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043391/0 /scratch/stefan/7916125/working/building/REAL250005043391 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/499
`/scratch/stefan/7916125/working/3D/499' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043391 none CC1=CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 59, 59, 59, 146, 201, 201, 201, 201, 201, 201, 201, 201, 59, 2, 2, 2, 1, 1, 13, 59, 59, 59, 59, 146, 146, 201, 201, 59, 59] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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])
total number of confs: 766
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043391 none CC1=CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [59, 59, 59, 6, 6, 6, 1, 1, 1, 1, 1, 7, 46, 46, 46, 67, 67, 67, 67, 67, 1, 59, 59, 59, 59, 59, 6, 1, 1, 1, 1, 7, 7, 46, 67, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 279
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043391 none CC1=CC1C(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 133, 133, 133, 67, 67, 67, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 133, 67, 67, 67, 67, 21, 21, 4, 1, 67, 67] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 621
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043391 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043391
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043391/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043391
Building REAL250005043392
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043392'
/scratch/stefan/7916125/working/building/REAL250005043392 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043392

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043392/0 /scratch/stefan/7916125/working/building/REAL250005043392 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/500
`/scratch/stefan/7916125/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043392 none C=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [35, 6, 6, 6, 1, 1, 1, 1, 1, 9, 49, 49, 49, 92, 92, 92, 92, 92, 1, 35, 35, 35, 6, 1, 1, 1, 1, 9, 9, 49, 92, 1, 1] 137
rigid atoms, others: [32, 4, 5, 6, 7, 8, 18, 23, 24, 25, 26, 31] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30])
total number of confs: 274
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043392 none C=CC(=O)NC1CC(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 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
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 137, 137, 92, 92, 92, 40, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 92, 137, 137, 137, 137, 92, 92, 92, 92, 40, 40, 7, 1, 92, 92] 137
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 438
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043392 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043392
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043392/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043392
Building REAL250005043393
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043393'
/scratch/stefan/7916125/working/building/REAL250005043393 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043393

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043393/0 /scratch/stefan/7916125/working/building/REAL250005043393 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/501
`/scratch/stefan/7916125/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1)

`REAL250005043393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043393 none CCC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 16, 16, 16, 16, 16, 1, 1, 1, 1, 22, 1, 1, 2, 2, 2, 1, 1] 51
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 38, 18, 19, 20, 21, 27, 28, 29, 30, 37] set([0, 1, 34, 3, 36, 11, 12, 13, 14, 15, 16, 17, 35, 22, 23, 24, 25, 26, 31])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043393 none CCC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [51, 40, 22, 40, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 51, 51, 51, 51, 51, 22, 22, 22, 22, 1, 22, 22, 22, 22, 22, 22, 22] 51
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 160
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043393 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043393
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043393/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043393
Building REAL250005043394
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043394'
/scratch/stefan/7916125/working/building/REAL250005043394 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043394

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043394/0 /scratch/stefan/7916125/working/building/REAL250005043394 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/502
`/scratch/stefan/7916125/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1)

`REAL250005043394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043394 none CC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 14, 1, 1, 2, 2, 2, 1, 1] 22
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 35] set([0, 32, 2, 33, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 28, 31])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043394 none CC(=O)N1C[C@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 22, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 22, 14, 14, 14, 14, 1, 14, 14, 14, 14, 14, 14, 14] 22
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 59
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043394 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043394
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043394/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043394
Building REAL250005043395
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043395'
/scratch/stefan/7916125/working/building/REAL250005043395 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043395

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043395/0 /scratch/stefan/7916125/working/building/REAL250005043395 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/503
`/scratch/stefan/7916125/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@]12CN(C(=O)CO)C[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043395 none C[C@]12CN(C(=O)CO)C[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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, 6, 6, 14, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1, 1, 14, 14, 42, 1, 1, 1, 1, 27, 1, 1] 135
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 13, 35, 21, 25, 26, 36, 30, 31] set([34, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29])
total number of confs: 131
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043395 none C[C@]12CN(C(=O)CO)C[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [27, 27, 27, 27, 27, 43, 43, 45, 27, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 45, 45, 135, 27, 27, 27, 27, 1, 27, 27] 135
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 253
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043395 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043395
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043395/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043395
Building REAL250005043396
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043396'
/scratch/stefan/7916125/working/building/REAL250005043396 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043396

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043396/0 /scratch/stefan/7916125/working/building/REAL250005043396 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/504
`/scratch/stefan/7916125/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1)

`REAL250005043396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043396 none CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 15, 15, 15, 16, 15, 1, 1, 1, 1, 22, 1, 1, 2, 2, 2, 1, 1] 52
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 38, 18, 19, 20, 21, 27, 28, 29, 30, 37] set([0, 1, 34, 3, 36, 11, 12, 13, 14, 15, 16, 17, 35, 22, 23, 24, 25, 26, 31])
total number of confs: 94
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043396 none CCC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 41, 22, 41, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 52, 52, 52, 52, 52, 22, 22, 22, 22, 1, 22, 22, 22, 22, 22, 22, 22] 52
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 162
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043396 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043396
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043396/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043396
Building REAL250005043397
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043397'
/scratch/stefan/7916125/working/building/REAL250005043397 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043397

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043397/0 /scratch/stefan/7916125/working/building/REAL250005043397 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/505
`/scratch/stefan/7916125/working/3D/505' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1)

`REAL250005043397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043397 none CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 13, 1, 1, 1, 1, 7, 7, 7, 1, 1, 1, 1, 13, 1, 1, 2, 2, 2, 1, 1] 23
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 35] set([0, 32, 2, 33, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 28, 31])
total number of confs: 42
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043397 none CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 23, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 23, 13, 13, 13, 13, 1, 13, 13, 13, 13, 13, 13, 13] 23
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 66
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043397 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043397
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043397/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043397
Building REAL250005043398
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043398'
/scratch/stefan/7916125/working/building/REAL250005043398 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043398

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043398/0 /scratch/stefan/7916125/working/building/REAL250005043398 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/506
`/scratch/stefan/7916125/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@]12CN(C(=O)CO)C[C@@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043398 none C[C@@]12CN(C(=O)CO)C[C@@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 19, 1, 1, 1, 1, 1, 1, 6, 6, 30, 31, 31, 31, 30, 1, 2, 2, 2, 1, 1, 19, 19, 57, 1, 1, 1, 1, 30, 1, 1] 138
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 8, 9, 10, 11, 12, 13, 35, 21, 25, 26, 36, 30, 31] set([34, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29])
total number of confs: 166
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043398 none C[C@@]12CN(C(=O)CO)C[C@@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 31, 31, 31, 40, 40, 46, 30, 30, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 30, 31, 31, 31, 31, 31, 46, 46, 138, 30, 30, 30, 30, 1, 30, 31] 138
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 264
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043398 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043398
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043398/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043398
Building REAL250005043399
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043399'
/scratch/stefan/7916125/working/building/REAL250005043399 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043399

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043399/0 /scratch/stefan/7916125/working/building/REAL250005043399 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/507
`/scratch/stefan/7916125/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1)

`REAL250005043399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043399 none C=CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 1, 1, 1, 1, 20, 1, 1, 2, 2, 2, 1, 1] 41
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 36, 18, 19, 20, 21, 25, 26, 27, 28, 30, 31] set([0, 1, 34, 3, 33, 32, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 29])
total number of confs: 87
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043399 none C=CC(=O)N1C[C@@H]2CN(C(=O)C3=CC(=O)[N-]O3)C[C@]2(C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 41, 20, 41, 20, 20, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 41, 41, 41, 20, 20, 20, 20, 1, 20, 20, 20, 20, 20, 20, 20] 41
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 102
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043399 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043399
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043399/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043399
Building REAL250005043400
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043400'
/scratch/stefan/7916125/working/building/REAL250005043400 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043400

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043400/0 /scratch/stefan/7916125/working/building/REAL250005043400 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/508
`/scratch/stefan/7916125/working/3D/508' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043400 none CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [130, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 130, 130, 130, 130, 130, 40, 9, 9, 1, 1, 26, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37])
total number of confs: 508
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043400 none CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 163, 163, 163, 89, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 201, 201, 201, 201, 201, 163, 89, 89, 26, 26, 1, 26, 26, 26, 26, 26] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 763
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043400 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043400
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043400/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043400
Building REAL250005043401
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043401'
/scratch/stefan/7916125/working/building/REAL250005043401 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043401

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043401/0 /scratch/stefan/7916125/working/building/REAL250005043401 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/509
`/scratch/stefan/7916125/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043401 none CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 1, 40, 40, 40, 40, 10, 10, 1, 1, 36, 1, 1, 2, 2, 2] 109
rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 160
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043401 none CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 36, 36, 36, 36, 9, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 109, 109, 109, 109, 95, 95, 36, 36, 1, 36, 36, 36, 36, 36] 109
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 360
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043401 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043401
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043401/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043401
Building REAL250005043402
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043402'
/scratch/stefan/7916125/working/building/REAL250005043402 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043402

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043402/0 /scratch/stefan/7916125/working/building/REAL250005043402 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/510
`/scratch/stefan/7916125/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1)

`REAL250005043402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043402 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 31, 31, 32, 120, 120, 2, 2, 2, 1, 1, 21, 1, 1, 8, 8, 32, 120, 120, 120, 120, 120] 173
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 355
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043402 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 67, 112, 112, 112, 173, 173, 21, 21, 21, 20, 20, 1, 21, 21, 67, 67, 112, 173, 173, 173, 173, 173] 173
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 573
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: REAL250005043402 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [122, 122, 122, 122, 122, 122, 169, 169, 175, 175, 175, 175, 175, 122, 57, 122, 12, 12, 1, 12, 1, 1, 1, 122, 122, 122, 122, 122, 175, 122, 122, 57, 57, 12, 1, 1, 1, 1, 1] 175
rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 573
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043402 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043402
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043402/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043402
Building REAL250005043403
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043403'
/scratch/stefan/7916125/working/building/REAL250005043403 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043403

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043403/0 /scratch/stefan/7916125/working/building/REAL250005043403 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/511
`/scratch/stefan/7916125/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043403 none COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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: [154, 131, 38, 38, 38, 8, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 154, 154, 154, 131, 131, 38, 8, 8, 1, 1, 20, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 544
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043403 none COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 143, 143, 143, 66, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 201, 201, 201, 201, 201, 143, 66, 66, 20, 20, 1, 20, 20, 20, 20, 20] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043403 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043403
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043403/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043403
Building REAL250005043404
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043404'
/scratch/stefan/7916125/working/building/REAL250005043404 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043404

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043404/0 /scratch/stefan/7916125/working/building/REAL250005043404 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/512
`/scratch/stefan/7916125/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043404 none CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 138, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 17, 16, 16, 1, 1, 1, 1, 165, 165, 165, 165, 165, 138, 138, 36, 9, 9, 1, 1, 17, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 729
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043404 none CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 127, 127, 127, 53, 17, 17, 17, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 201, 201, 201, 201, 201, 197, 197, 127, 53, 53, 16, 17, 1, 16, 16, 17, 17, 17] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 788
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043404 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043404
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043404/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043404
Building REAL250005043405
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043405'
/scratch/stefan/7916125/working/building/REAL250005043405 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043405

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043405/0 /scratch/stefan/7916125/working/building/REAL250005043405 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/513
`/scratch/stefan/7916125/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043405 none CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [117, 39, 117, 39, 39, 9, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 39, 9, 9, 1, 1, 22, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 469
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043405 none CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 174, 201, 174, 174, 87, 23, 23, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 201, 201, 201, 201, 201, 201, 201, 174, 87, 87, 22, 22, 1, 22, 23, 23, 23, 23] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043405 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043405
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043405/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043405
Building REAL250005043406
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043406'
/scratch/stefan/7916125/working/building/REAL250005043406 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043406

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043406/0 /scratch/stefan/7916125/working/building/REAL250005043406 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/514
`/scratch/stefan/7916125/working/3D/514' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O)

`REAL250005043406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043406 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 31, 32, 32, 32, 32, 1, 1, 1, 1, 10, 41, 41, 41, 74, 74, 2, 2, 2, 1, 1, 31, 1, 1, 10, 10, 41, 74, 74] 154
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35])
total number of confs: 262
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043406 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 32, 32, 31, 96, 150, 150, 150, 154, 154, 32, 32, 32, 32, 32, 1, 31, 31, 96, 96, 150, 154, 154] 154
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 509
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043406 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043406
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043406/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043406
Building REAL250005043407
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043407'
/scratch/stefan/7916125/working/building/REAL250005043407 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043407

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043407/0 /scratch/stefan/7916125/working/building/REAL250005043407 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/515
`/scratch/stefan/7916125/working/3D/515' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043407 none C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [165, 129, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 1, 165, 165, 165, 129, 129, 35, 7, 7, 1, 1, 13, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043407 none C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 127, 127, 127, 51, 14, 14, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 201, 201, 201, 201, 201, 127, 51, 51, 13, 13, 1, 14, 14, 14, 14, 14] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043407 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043407
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043407/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043407
Building REAL250005043408
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043408'
/scratch/stefan/7916125/working/building/REAL250005043408 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043408

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043408/0 /scratch/stefan/7916125/working/building/REAL250005043408 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/516
`/scratch/stefan/7916125/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO)

`REAL250005043408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043408 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 28, 28, 1, 1, 1, 1, 9, 34, 34, 34, 74, 2, 2, 2, 1, 1, 27, 1, 1, 9, 9, 34, 76, 76, 228] 348
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 555
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043408 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 28, 27, 72, 113, 113, 113, 116, 28, 28, 28, 28, 28, 1, 27, 27, 72, 72, 113, 116, 116, 348] 348
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 754
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043408 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043408
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043408/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043408
Building REAL250005043409
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043409'
/scratch/stefan/7916125/working/building/REAL250005043409 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043409

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043409/0 /scratch/stefan/7916125/working/building/REAL250005043409 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/517
`/scratch/stefan/7916125/working/3D/517' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043409 none CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [129, 38, 125, 38, 38, 9, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 129, 129, 129, 129, 387, 38, 9, 9, 1, 1, 29, 1, 1, 2, 2, 2] 603
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043409 none CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 199, 187, 187, 106, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 201, 201, 201, 201, 603, 187, 106, 106, 29, 29, 1, 29, 29, 29, 29, 29] 603
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 1310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043409 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043409
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043409/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043409
Building REAL250005043410
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043410'
/scratch/stefan/7916125/working/building/REAL250005043410 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043410

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043410/0 /scratch/stefan/7916125/working/building/REAL250005043410 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/518
`/scratch/stefan/7916125/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF)

`REAL250005043410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043410 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 6, 6, 14, 14, 14, 15, 15, 1, 1, 1, 1, 8, 33, 33, 33, 137, 164, 2, 2, 2, 1, 1, 14, 1, 1, 8, 8, 33, 137, 137, 164, 164] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 674
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043410 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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: [15, 15, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 15, 15, 14, 50, 117, 117, 117, 201, 201, 15, 15, 15, 15, 15, 1, 14, 14, 50, 50, 117, 201, 201, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 777
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043410 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043410
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043410/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043410
Building REAL250005043411
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043411'
/scratch/stefan/7916125/working/building/REAL250005043411 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043411

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043411/0 /scratch/stefan/7916125/working/building/REAL250005043411 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/519
`/scratch/stefan/7916125/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043411 none C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
411  conformations in input
total number of sets (complete confs): 411
using faster count positions algorithm for large data
unique positions, atoms: [102, 37, 102, 101, 37, 37, 10, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 102, 102, 102, 306, 37, 10, 10, 1, 1, 23, 1, 1, 2, 2, 2] 411
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 717
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043411 none C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
411  conformations in input
total number of sets (complete confs): 411
using faster count positions algorithm for large data
unique positions, atoms: [137, 120, 137, 137, 120, 120, 70, 23, 23, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 137, 137, 137, 411, 120, 70, 70, 22, 22, 1, 23, 23, 23, 23, 23] 411
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 894
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043411 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043411
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043411/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043411
Building REAL250005043412
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043412'
/scratch/stefan/7916125/working/building/REAL250005043412 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043412

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043412/0 /scratch/stefan/7916125/working/building/REAL250005043412 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/520
`/scratch/stefan/7916125/working/3D/520' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043412 none C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [132, 42, 132, 127, 42, 42, 10, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 132, 132, 132, 396, 42, 10, 10, 1, 1, 31, 1, 1, 2, 2, 2] 603
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 922
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043412 none C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 201, 201, 187, 187, 110, 31, 31, 31, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 201, 201, 201, 603, 187, 110, 110, 31, 31, 1, 31, 31, 31, 31, 31] 603
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 1313
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043412 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043412
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043412/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043412
Building REAL250005043413
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043413'
/scratch/stefan/7916125/working/building/REAL250005043413 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043413

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043413/0 /scratch/stefan/7916125/working/building/REAL250005043413 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/521
`/scratch/stefan/7916125/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043413 none CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [104, 104, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 104, 104, 104, 104, 104, 39, 8, 8, 1, 1, 29, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 333
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043413 none CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 172, 172, 172, 94, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 201, 201, 201, 201, 201, 172, 94, 94, 29, 29, 1, 29, 29, 29, 29, 29] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 681
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043413 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043413
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043413/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043413
Building REAL250005043414
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043414'
/scratch/stefan/7916125/working/building/REAL250005043414 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043414

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043414/0 /scratch/stefan/7916125/working/building/REAL250005043414 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/522
`/scratch/stefan/7916125/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043414 none COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 6, 1, 6, 1, 1, 1, 1, 1, 9, 46, 46, 46, 70, 70, 70, 70, 70, 1, 1, 1, 1, 60, 60, 60, 25, 25, 1, 1, 9, 9, 46, 70, 2, 2, 2, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 301
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043414 none COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 110, 70, 110, 70, 70, 24, 70, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 201, 201, 201, 196, 196, 70, 70, 24, 24, 5, 1, 70, 70, 70, 70, 70] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 780
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043414 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043414
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043414/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043414
Building REAL250005043415
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043415'
/scratch/stefan/7916125/working/building/REAL250005043415 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043415

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043415/0 /scratch/stefan/7916125/working/building/REAL250005043415 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/523
`/scratch/stefan/7916125/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043415 none CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 28, 6, 1, 6, 1, 1, 1, 1, 1, 10, 44, 44, 44, 72, 72, 72, 72, 72, 1, 1, 1, 1, 45, 45, 45, 44, 44, 28, 28, 1, 1, 10, 10, 44, 72, 2, 2, 2, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 394
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043415 none CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 123, 72, 123, 72, 72, 28, 72, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 201, 201, 201, 201, 201, 198, 198, 72, 72, 28, 28, 7, 1, 72, 72, 72, 72, 72] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043415 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043415
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043415/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043415
Building REAL250005043416
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043416'
/scratch/stefan/7916125/working/building/REAL250005043416 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043416

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043416/0 /scratch/stefan/7916125/working/building/REAL250005043416 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/524
`/scratch/stefan/7916125/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043416 none CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 10, 43, 43, 43, 62, 62, 62, 62, 62, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 10, 10, 43, 62, 2, 2, 2, 1, 1] 89
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 205
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043416 none CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 62, 89, 62, 62, 28, 62, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 89, 89, 89, 89, 89, 89, 89, 62, 62, 28, 28, 7, 1, 62, 62, 62, 62, 62] 89
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 292
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043416 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043416
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043416/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043416
Building REAL250005043417
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043417'
/scratch/stefan/7916125/working/building/REAL250005043417 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043417

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043417/0 /scratch/stefan/7916125/working/building/REAL250005043417 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/525
`/scratch/stefan/7916125/working/3D/525' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043417 none CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 10, 50, 50, 50, 71, 71, 71, 71, 71, 1, 1, 1, 1, 18, 18, 18, 18, 18, 1, 1, 10, 10, 50, 71, 2, 2, 2, 1, 1] 114
rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 19, 20, 21, 36, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 236
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043417 none CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 103, 71, 103, 71, 71, 29, 71, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 114, 114, 114, 114, 114, 71, 71, 29, 29, 8, 1, 71, 71, 71, 71, 71] 114
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 388
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043417 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043417
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043417/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043417
Building REAL250005043418
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043418'
/scratch/stefan/7916125/working/building/REAL250005043418 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043418

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043418/0 /scratch/stefan/7916125/working/building/REAL250005043418 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/526
`/scratch/stefan/7916125/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043418 none CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 30, 30, 30, 42, 42, 42, 42, 42, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 30, 42, 2, 2, 2, 1, 1] 53
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 24, 25, 33] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 116
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043418 none CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 42, 53, 42, 42, 31, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 53, 53, 53, 42, 42, 30, 30, 8, 1, 42, 42, 42, 42, 42] 53
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 189
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043418 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043418
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043418/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043418
Building REAL250005043419
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043419'
/scratch/stefan/7916125/working/building/REAL250005043419 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043419

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043419/0 /scratch/stefan/7916125/working/building/REAL250005043419 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/527
`/scratch/stefan/7916125/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043419 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 6, 28, 28, 1, 1, 1, 1, 9, 46, 46, 46, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 28, 28, 28, 28, 28, 1, 1, 9, 9, 46, 80] 135
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 10, 11, 12, 34, 13, 26, 27] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043419 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 28, 28, 28, 28, 79, 127, 127, 127, 135, 135, 135, 135, 135, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 28, 28, 79, 79, 127, 135] 135
rigid atoms, others: [32, 5, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 433
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043419 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [80, 80, 80, 80, 80, 80, 98, 98, 135, 135, 80, 36, 80, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 135, 135, 135, 135, 135, 80, 80, 36, 36, 7, 1] 135
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 468
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043419 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043419
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043419/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043419
Building REAL250005043420
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043420'
/scratch/stefan/7916125/working/building/REAL250005043420 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043420

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043420/0 /scratch/stefan/7916125/working/building/REAL250005043420 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/528
`/scratch/stefan/7916125/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043420 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 1, 1, 1, 1, 7, 20, 20, 20, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 12, 12, 1, 1, 7, 7, 20, 26] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 26, 27, 30, 31] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043420 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 26, 26, 26, 26, 26, 28, 28, 36, 36, 26, 16, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 36, 36, 26, 26, 16, 16, 7, 1] 36
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043420 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043420
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043420/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043420
Building REAL250005043421
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043421'
/scratch/stefan/7916125/working/building/REAL250005043421 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043421

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043421/0 /scratch/stefan/7916125/working/building/REAL250005043421 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/529
`/scratch/stefan/7916125/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043421 none C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 17, 1, 1, 1, 1, 9, 37, 37, 37, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 17, 17, 51, 1, 1, 9, 9, 37, 51] 240
rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 25, 26, 30, 31] set([6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 233
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043421 none C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 69, 69, 80, 51, 24, 51, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 80, 80, 240, 51, 51, 24, 24, 8, 1] 240
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 532
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043421 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043421
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043421/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043421
Building REAL250005043422
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043422'
/scratch/stefan/7916125/working/building/REAL250005043422 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043422

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043422/0 /scratch/stefan/7916125/working/building/REAL250005043422 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/530
`/scratch/stefan/7916125/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043422 none CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [19, 4, 19, 1, 4, 1, 1, 1, 1, 1, 8, 31, 31, 31, 35, 35, 35, 35, 35, 1, 1, 1, 1, 19, 19, 19, 19, 57, 1, 1, 8, 8, 31, 35, 2, 2, 2, 1, 1] 282
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 220
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043422 none CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [94, 51, 94, 35, 51, 35, 35, 19, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 94, 94, 94, 94, 282, 35, 35, 18, 18, 5, 1, 35, 35, 35, 35, 35] 282
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 663
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043422 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043422
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043422/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043422
Building REAL250005043423
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043423'
/scratch/stefan/7916125/working/building/REAL250005043423 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043423

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043423/0 /scratch/stefan/7916125/working/building/REAL250005043423 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/531
`/scratch/stefan/7916125/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043423 none CC(=O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 16, 1, 4, 1, 1, 1, 1, 1, 9, 32, 32, 32, 42, 42, 42, 42, 42, 1, 1, 1, 1, 16, 16, 16, 1, 1, 9, 9, 32, 42, 2, 2, 2, 1, 1] 65
rigid atoms, others: [35, 3, 36, 5, 6, 7, 8, 9, 19, 20, 21, 22, 26, 27] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 155
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043423 none CC(=O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 50, 65, 42, 50, 42, 42, 18, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 65, 65, 65, 42, 42, 18, 18, 7, 1, 42, 42, 42, 42, 42] 65
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043423 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043423
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043423/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043423
Building REAL250005043424
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043424'
/scratch/stefan/7916125/working/building/REAL250005043424 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043424

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043424/0 /scratch/stefan/7916125/working/building/REAL250005043424 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/532
`/scratch/stefan/7916125/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043424 none CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [28, 27, 6, 1, 6, 1, 1, 1, 1, 1, 9, 42, 42, 42, 53, 53, 53, 53, 53, 1, 1, 1, 1, 28, 28, 28, 27, 28, 1, 1, 9, 9, 42, 53, 2, 2, 2, 1, 1] 106
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 203
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043424 none CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 90, 53, 90, 53, 53, 22, 53, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 106, 106, 106, 106, 106, 53, 53, 22, 22, 6, 1, 53, 53, 53, 53, 53] 106
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 344
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043424 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043424
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043424/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043424
Building REAL250005043425
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043425'
/scratch/stefan/7916125/working/building/REAL250005043425 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043425

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043425/0 /scratch/stefan/7916125/working/building/REAL250005043425 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/533
`/scratch/stefan/7916125/working/3D/533' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043425 none C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
300  conformations in input
total number of sets (complete confs): 300
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 19, 1, 7, 1, 1, 1, 1, 1, 10, 41, 41, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 19, 19, 19, 57, 1, 1, 10, 10, 41, 50, 2, 2, 2, 1, 1] 300
rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 21, 22, 23, 38, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 250
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043425 none C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
300  conformations in input
total number of sets (complete confs): 300
using faster count positions algorithm for large data
unique positions, atoms: [100, 67, 100, 100, 50, 67, 50, 50, 22, 50, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 100, 100, 300, 50, 50, 22, 22, 6, 1, 50, 50, 50, 50, 50] 300
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 680
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043425 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043425
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043425/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043425
Building REAL250005043426
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043426'
/scratch/stefan/7916125/working/building/REAL250005043426 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043426

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043426/0 /scratch/stefan/7916125/working/building/REAL250005043426 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/534
`/scratch/stefan/7916125/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043426 none C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 27, 5, 1, 5, 1, 1, 1, 1, 1, 9, 43, 43, 43, 73, 73, 73, 73, 73, 1, 1, 1, 1, 66, 66, 66, 27, 27, 1, 1, 9, 9, 43, 73, 2, 2, 2, 1, 1] 194
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043426 none C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 122, 73, 122, 73, 73, 30, 73, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 194, 194, 194, 194, 194, 73, 73, 30, 30, 9, 1, 73, 73, 73, 73, 73] 194
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043426 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043426
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043426/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043426
Building REAL250005043427
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043427'
/scratch/stefan/7916125/working/building/REAL250005043427 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043427

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043427/0 /scratch/stefan/7916125/working/building/REAL250005043427 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/535
`/scratch/stefan/7916125/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CC#N)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043427 none C[C@@H]1CN(C(=O)CC#N)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 5, 5, 27, 27, 1, 1, 1, 1, 9, 39, 39, 39, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 27, 27, 1, 1, 9, 9, 39, 59] 142
rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 26, 27, 30, 31] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 227
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043427 none C[C@@H]1CN(C(=O)CC#N)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [59, 59, 59, 59, 59, 59, 89, 89, 142, 142, 59, 26, 59, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 142, 142, 59, 59, 26, 26, 10, 1] 142
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 549
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043427 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043427
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043427/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043427
Building REAL250005043428
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043428'
/scratch/stefan/7916125/working/building/REAL250005043428 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043428

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043428/0 /scratch/stefan/7916125/working/building/REAL250005043428 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/536
`/scratch/stefan/7916125/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043428 none C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 28, 45, 1, 1, 1, 1, 9, 43, 43, 43, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 28, 28, 45, 45, 1, 1, 9, 9, 43, 67] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 26, 27] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 338
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043428 none C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 112, 112, 201, 201, 67, 23, 67, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 201, 201, 201, 201, 67, 67, 23, 23, 5, 1] 201
rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 769
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043428 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043428
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043428/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043428
Building REAL250005043429
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043429'
/scratch/stefan/7916125/working/building/REAL250005043429 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043429

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043429/0 /scratch/stefan/7916125/working/building/REAL250005043429 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/537
`/scratch/stefan/7916125/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043429 none C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [16, 5, 16, 16, 1, 5, 1, 1, 1, 1, 1, 7, 30, 30, 30, 36, 36, 36, 36, 36, 1, 1, 1, 1, 16, 16, 16, 48, 1, 1, 7, 7, 30, 36, 2, 2, 2, 1, 1] 243
rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 21, 22, 23, 38, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 198
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043429 none C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [81, 49, 81, 81, 36, 49, 36, 36, 17, 36, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 81, 81, 81, 243, 36, 36, 16, 16, 7, 1, 36, 36, 36, 36, 36] 243
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 567
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043429 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043429
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043429/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043429
Building REAL250005043430
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043430'
/scratch/stefan/7916125/working/building/REAL250005043430 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043430

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043430/0 /scratch/stefan/7916125/working/building/REAL250005043430 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/538
`/scratch/stefan/7916125/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043430 none C=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [24, 6, 1, 6, 1, 1, 1, 1, 1, 9, 48, 48, 48, 65, 65, 65, 65, 65, 1, 1, 1, 1, 24, 24, 24, 1, 1, 9, 9, 48, 65, 2, 2, 2, 1, 1] 87
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 34, 18, 19, 20, 21, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 213
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043430 none C=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 87, 65, 87, 65, 65, 26, 65, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 87, 87, 87, 65, 65, 26, 26, 7, 1, 65, 65, 65, 65, 65] 87
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 276
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043430 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043430
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043430/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043430
Building REAL250005043431
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043431'
/scratch/stefan/7916125/working/building/REAL250005043431 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043431

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043431/0 /scratch/stefan/7916125/working/building/REAL250005043431 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/539
`/scratch/stefan/7916125/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043431 none CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [101, 37, 37, 37, 9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 101, 101, 101, 101, 101, 37, 9, 9, 5, 5, 1, 1, 25, 1, 1, 2, 2, 2] 160
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 423
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043431 none CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [160, 129, 129, 129, 77, 41, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 160, 160, 160, 160, 160, 129, 77, 77, 41, 41, 24, 24, 1, 25, 25, 25, 25, 25] 160
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 674
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043431 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043431
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043431/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043431
Building REAL250005043432
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043432'
/scratch/stefan/7916125/working/building/REAL250005043432 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043432

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043432/0 /scratch/stefan/7916125/working/building/REAL250005043432 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/540
`/scratch/stefan/7916125/working/3D/540' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043432 none CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 29, 29, 29, 29, 9, 9, 5, 5, 1, 1, 20, 1, 1, 2, 2, 2] 66
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37])
total number of confs: 127
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043432 none CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 48, 31, 20, 20, 20, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 66, 66, 66, 66, 48, 48, 31, 31, 19, 19, 1, 20, 20, 20, 20, 20] 66
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 257
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043432 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043432
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043432/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043432
Building REAL250005043433
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043433'
/scratch/stefan/7916125/working/building/REAL250005043433 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043433

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043433/0 /scratch/stefan/7916125/working/building/REAL250005043433 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/541
`/scratch/stefan/7916125/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO)

`REAL250005043433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043433 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 10, 10, 1, 1, 1, 1, 4, 5, 8, 8, 8, 20, 2, 2, 2, 1, 1, 11, 1, 1, 4, 4, 5, 5, 8, 20, 20, 60] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 159
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043433 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [11, 11, 11, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 23, 23, 23, 24, 11, 11, 11, 10, 10, 1, 11, 11, 15, 15, 15, 15, 23, 24, 24, 72] 72
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 148
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043433 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043433
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043433/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043433
Building REAL250005043434
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043434'
/scratch/stefan/7916125/working/building/REAL250005043434 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043434

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043434/0 /scratch/stefan/7916125/working/building/REAL250005043434 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/542
`/scratch/stefan/7916125/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043434 none CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 64, 64, 64, 99, 99, 99, 99, 99, 1, 20, 20, 20, 19, 19, 1, 1, 2, 2, 2, 6, 6, 11, 11, 64, 99, 1, 1] 162
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 40, 22, 39, 28, 29] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043434 none CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [162, 144, 99, 144, 99, 99, 99, 99, 99, 49, 99, 38, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 99, 162, 162, 162, 162, 162, 99, 99, 99, 99, 99, 64, 64, 38, 38, 9, 1, 99, 99] 162
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 677
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043434 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043434
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043434/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043434
Building REAL250005043435
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043435'
/scratch/stefan/7916125/working/building/REAL250005043435 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043435

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043435/0 /scratch/stefan/7916125/working/building/REAL250005043435 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/543
`/scratch/stefan/7916125/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043435 none CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 40, 40, 40, 56, 56, 56, 56, 56, 1, 6, 6, 6, 1, 1, 2, 2, 2, 7, 7, 13, 13, 40, 56, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 37, 36] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 174
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043435 none CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 56, 77, 56, 56, 56, 56, 56, 33, 56, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 56, 77, 77, 77, 56, 56, 56, 56, 56, 40, 40, 27, 27, 7, 1, 56, 56] 77
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 323
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043435 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043435
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043435/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043435
Building REAL250005043436
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043436'
/scratch/stefan/7916125/working/building/REAL250005043436 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043436

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043436/0 /scratch/stefan/7916125/working/building/REAL250005043436 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/544
`/scratch/stefan/7916125/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043436 none C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
363  conformations in input
total number of sets (complete confs): 363
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 1, 1, 1, 1, 6, 12, 51, 51, 51, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 15, 15, 45, 1, 1, 6, 6, 12, 12, 51, 72] 363
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10, 11, 12, 26, 27, 31] set([6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 286
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043436 none C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
363  conformations in input
total number of sets (complete confs): 363
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 103, 103, 121, 72, 38, 72, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 121, 121, 363, 72, 72, 48, 48, 30, 30, 8, 1] 363
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 888
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043436 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043436
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043436/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043436
Building REAL250005043437
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043437'
/scratch/stefan/7916125/working/building/REAL250005043437 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043437

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043437/0 /scratch/stefan/7916125/working/building/REAL250005043437 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/545
`/scratch/stefan/7916125/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043437 none C=CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 52, 52, 52, 70, 70, 70, 70, 70, 1, 22, 22, 22, 1, 1, 2, 2, 2, 6, 6, 11, 11, 52, 70, 1, 1] 105
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 38, 22, 26, 27, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 240
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043437 none C=CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 70, 105, 70, 70, 70, 70, 70, 37, 70, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 70, 105, 105, 105, 70, 70, 70, 70, 70, 47, 47, 27, 27, 6, 1, 70, 70] 105
rigid atoms, others: [36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 415
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043437 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043437
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043437/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043437
Building REAL250005043438
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043438'
/scratch/stefan/7916125/working/building/REAL250005043438 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043438

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043438/0 /scratch/stefan/7916125/working/building/REAL250005043438 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/546
`/scratch/stefan/7916125/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043438 none CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 64, 64, 64, 99, 99, 99, 99, 99, 1, 20, 20, 20, 19, 19, 1, 1, 2, 2, 2, 6, 6, 11, 11, 64, 99, 1, 1] 162
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 40, 22, 39, 28, 29] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 306
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043438 none CCC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
162  conformations in input
total number of sets (complete confs): 162
using faster count positions algorithm for large data
unique positions, atoms: [162, 144, 99, 144, 99, 99, 99, 99, 99, 49, 99, 38, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 99, 162, 162, 162, 162, 162, 99, 99, 99, 99, 99, 64, 64, 38, 38, 9, 1, 99, 99] 162
rigid atoms, others: [38, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 677
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043438 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043438
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043438/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043438
Building REAL250005043439
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043439'
/scratch/stefan/7916125/working/building/REAL250005043439 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043439

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043439/0 /scratch/stefan/7916125/working/building/REAL250005043439 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/547
`/scratch/stefan/7916125/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043439 none CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 40, 40, 40, 56, 56, 56, 56, 56, 1, 6, 6, 6, 1, 1, 2, 2, 2, 7, 7, 13, 13, 40, 56, 1, 1] 77
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 25, 26, 37, 36] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 174
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043439 none CC(=O)N1C[C@@H](C)[C@H](CCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [77, 56, 77, 56, 56, 56, 56, 56, 33, 56, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 56, 77, 77, 77, 56, 56, 56, 56, 56, 40, 40, 27, 27, 7, 1, 56, 56] 77
rigid atoms, others: [35, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 323
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043439 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043439
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043439/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043439
Building REAL250005043440
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043440'
/scratch/stefan/7916125/working/building/REAL250005043440 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043440

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043440/0 /scratch/stefan/7916125/working/building/REAL250005043440 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/548
`/scratch/stefan/7916125/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043440 none C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
363  conformations in input
total number of sets (complete confs): 363
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 15, 1, 1, 1, 1, 6, 12, 51, 51, 51, 72, 72, 72, 72, 72, 2, 2, 2, 1, 1, 15, 15, 45, 1, 1, 6, 6, 12, 12, 51, 72] 363
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 9, 10, 11, 12, 26, 27, 31] set([6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 33, 34, 35, 36, 37, 38])
total number of confs: 286
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043440 none C[C@@H]1CN(C(=O)CO)C[C@H]1CCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
363  conformations in input
total number of sets (complete confs): 363
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 72, 72, 103, 103, 121, 72, 38, 72, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 121, 121, 363, 72, 72, 48, 48, 30, 30, 8, 1] 363
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 888
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043440 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043440
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043440/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043440
Building REAL250005043441
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043441'
/scratch/stefan/7916125/working/building/REAL250005043441 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043441

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043441/0 /scratch/stefan/7916125/working/building/REAL250005043441 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/549
`/scratch/stefan/7916125/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043441 none CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [101, 37, 37, 37, 9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 1, 1, 101, 101, 101, 101, 101, 37, 9, 9, 5, 5, 1, 1, 25, 1, 1, 2, 2, 2] 160
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 423
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043441 none CCC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
160  conformations in input
total number of sets (complete confs): 160
using faster count positions algorithm for large data
unique positions, atoms: [160, 129, 129, 129, 77, 41, 25, 25, 25, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 160, 160, 160, 160, 160, 129, 77, 77, 41, 41, 24, 24, 1, 25, 25, 25, 25, 25] 160
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 674
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043441 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043441
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043441/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043441
Building REAL250005043442
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043442'
/scratch/stefan/7916125/working/building/REAL250005043442 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043442

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043442/0 /scratch/stefan/7916125/working/building/REAL250005043442 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/550
`/scratch/stefan/7916125/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043442 none CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 9, 5, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 1, 1, 1, 1, 29, 29, 29, 29, 9, 9, 5, 5, 1, 1, 20, 1, 1, 2, 2, 2] 66
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37])
total number of confs: 127
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043442 none CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 48, 31, 20, 20, 20, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 66, 66, 66, 66, 48, 48, 31, 31, 19, 19, 1, 20, 20, 20, 20, 20] 66
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 257
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043442 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043442
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043442/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043442
Building REAL250005043443
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043443'
/scratch/stefan/7916125/working/building/REAL250005043443 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043443

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043443/0 /scratch/stefan/7916125/working/building/REAL250005043443 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/551
`/scratch/stefan/7916125/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO)

`REAL250005043443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043443 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 10, 10, 1, 1, 1, 1, 4, 5, 8, 8, 8, 20, 2, 2, 2, 1, 1, 11, 1, 1, 4, 4, 5, 5, 8, 20, 20, 60] 72
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 159
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043443 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CCNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [11, 11, 11, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 23, 23, 23, 24, 11, 11, 11, 10, 10, 1, 11, 11, 15, 15, 15, 15, 23, 24, 24, 72] 72
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 148
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043443 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043443
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043443/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043443
Building REAL250005043444
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043444'
/scratch/stefan/7916125/working/building/REAL250005043444 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043444

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043444/0 /scratch/stefan/7916125/working/building/REAL250005043444 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/552
`/scratch/stefan/7916125/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043444 none C=CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [99, 53, 53, 53, 11, 6, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 99, 99, 99, 53, 11, 11, 6, 6, 1, 1, 28, 1, 1, 2, 2, 2] 183
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 347
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043444 none C=CC(=O)NCC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [183, 183, 183, 183, 118, 73, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 183, 183, 183, 183, 118, 118, 73, 73, 28, 28, 1, 28, 28, 28, 28, 28] 183
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 706
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043444 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043444
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043444/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043444
Building REAL250005043445
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043445'
/scratch/stefan/7916125/working/building/REAL250005043445 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043445

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043445/0 /scratch/stefan/7916125/working/building/REAL250005043445 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/553
`/scratch/stefan/7916125/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043445 none CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [17, 6, 1, 6, 1, 1, 1, 1, 1, 10, 50, 50, 50, 71, 71, 71, 71, 71, 1, 1, 1, 1, 18, 18, 18, 18, 18, 1, 1, 10, 10, 50, 71, 2, 2, 2, 1, 1] 114
rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 19, 20, 21, 36, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 236
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043445 none CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 103, 71, 103, 71, 71, 29, 71, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 114, 114, 114, 114, 114, 71, 71, 29, 29, 8, 1, 71, 71, 71, 71, 71] 114
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 388
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043445 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043445
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043445/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043445
Building REAL250005043446
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043446'
/scratch/stefan/7916125/working/building/REAL250005043446 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043446

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043446/0 /scratch/stefan/7916125/working/building/REAL250005043446 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/554
`/scratch/stefan/7916125/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043446 none CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 9, 30, 30, 30, 42, 42, 42, 42, 42, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 30, 42, 2, 2, 2, 1, 1] 53
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 17, 18, 19, 20, 24, 25, 33] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30, 31])
total number of confs: 116
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043446 none CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
53  conformations in input
total number of sets (complete confs): 53
using faster count positions algorithm for large data
unique positions, atoms: [53, 42, 53, 42, 42, 31, 42, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 53, 53, 53, 42, 42, 30, 30, 8, 1, 42, 42, 42, 42, 42] 53
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 189
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043446 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043446
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043446/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043446
Building REAL250005043447
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043447'
/scratch/stefan/7916125/working/building/REAL250005043447 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043447

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043447/0 /scratch/stefan/7916125/working/building/REAL250005043447 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/555
`/scratch/stefan/7916125/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043447 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 6, 28, 28, 1, 1, 1, 1, 9, 46, 46, 46, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 28, 28, 28, 28, 28, 1, 1, 9, 9, 46, 80] 135
rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 10, 11, 12, 34, 13, 26, 27] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 35, 36, 37, 38])
total number of confs: 249
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043447 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 28, 28, 28, 28, 79, 127, 127, 127, 135, 135, 135, 135, 135, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 28, 28, 79, 79, 127, 135] 135
rigid atoms, others: [32, 5, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 433
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043447 none C[C@@H]1CN(C(=O)C2CC2)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [80, 80, 80, 80, 80, 80, 98, 98, 135, 135, 80, 36, 80, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 135, 135, 135, 135, 135, 80, 80, 36, 36, 7, 1] 135
rigid atoms, others: [38, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 468
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043447 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043447
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043447/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043447
Building REAL250005043448
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043448'
/scratch/stefan/7916125/working/building/REAL250005043448 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043448

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043448/0 /scratch/stefan/7916125/working/building/REAL250005043448 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/556
`/scratch/stefan/7916125/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043448 none COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 6, 1, 6, 1, 1, 1, 1, 1, 9, 46, 46, 46, 70, 70, 70, 70, 70, 1, 1, 1, 1, 60, 60, 60, 25, 25, 1, 1, 9, 9, 46, 70, 2, 2, 2, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 301
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043448 none COCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 110, 70, 110, 70, 70, 24, 70, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 201, 201, 201, 196, 196, 70, 70, 24, 24, 5, 1, 70, 70, 70, 70, 70] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 780
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043448 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043448
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043448/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043448
Building REAL250005043449
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043449'
/scratch/stefan/7916125/working/building/REAL250005043449 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043449

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043449/0 /scratch/stefan/7916125/working/building/REAL250005043449 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/557
`/scratch/stefan/7916125/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043449 none CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 28, 6, 1, 6, 1, 1, 1, 1, 1, 10, 44, 44, 44, 72, 72, 72, 72, 72, 1, 1, 1, 1, 45, 45, 45, 44, 44, 28, 28, 1, 1, 10, 10, 44, 72, 2, 2, 2, 1, 1] 201
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 394
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043449 none CCCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 123, 72, 123, 72, 72, 28, 72, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 201, 201, 201, 201, 201, 198, 198, 72, 72, 28, 28, 7, 1, 72, 72, 72, 72, 72] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 761
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043449 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043449
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043449/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043449
Building REAL250005043450
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043450'
/scratch/stefan/7916125/working/building/REAL250005043450 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043450

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043450/0 /scratch/stefan/7916125/working/building/REAL250005043450 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/558
`/scratch/stefan/7916125/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043450 none CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 15, 1, 7, 1, 1, 1, 1, 1, 10, 43, 43, 43, 62, 62, 62, 62, 62, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1, 10, 10, 43, 62, 2, 2, 2, 1, 1] 89
rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 205
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043450 none CC(C)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 62, 89, 62, 62, 28, 62, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 89, 89, 89, 89, 89, 89, 89, 62, 62, 28, 28, 7, 1, 62, 62, 62, 62, 62] 89
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 292
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043450 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043450
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043450/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043450
Building REAL250005043451
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043451'
/scratch/stefan/7916125/working/building/REAL250005043451 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043451

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043451/0 /scratch/stefan/7916125/working/building/REAL250005043451 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/559
`/scratch/stefan/7916125/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043451 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 1, 1, 1, 1, 7, 20, 20, 20, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 12, 12, 1, 1, 7, 7, 20, 26] 36
rigid atoms, others: [0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 26, 27, 30, 31] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 32, 33, 34, 35])
total number of confs: 98
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043451 none C[C@@H]1CN(C(=O)C(N)=O)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [26, 26, 26, 26, 26, 26, 28, 28, 36, 36, 26, 16, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 36, 36, 26, 26, 16, 16, 7, 1] 36
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 119
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043451 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043451
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043451/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043451
Building REAL250005043452
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043452'
/scratch/stefan/7916125/working/building/REAL250005043452 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043452

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043452/0 /scratch/stefan/7916125/working/building/REAL250005043452 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/560
`/scratch/stefan/7916125/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043452 none C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [66, 27, 5, 1, 5, 1, 1, 1, 1, 1, 9, 43, 43, 43, 73, 73, 73, 73, 73, 1, 1, 1, 1, 66, 66, 66, 27, 27, 1, 1, 9, 9, 43, 73, 2, 2, 2, 1, 1] 194
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 372
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043452 none C=CCC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 122, 73, 122, 73, 73, 30, 73, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 194, 194, 194, 194, 194, 73, 73, 30, 30, 9, 1, 73, 73, 73, 73, 73] 194
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 741
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043452 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043452
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043452/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043452
Building REAL250005043453
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043453'
/scratch/stefan/7916125/working/building/REAL250005043453 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043453

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043453/0 /scratch/stefan/7916125/working/building/REAL250005043453 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/561
`/scratch/stefan/7916125/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043453 none C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 17, 1, 1, 1, 1, 9, 37, 37, 37, 51, 51, 51, 51, 51, 2, 2, 2, 1, 1, 17, 17, 51, 1, 1, 9, 9, 37, 51] 240
rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 25, 26, 30, 31] set([6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35])
total number of confs: 233
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043453 none C[C@@H]1CN(C(=O)CO)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 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]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [51, 51, 51, 51, 51, 51, 69, 69, 80, 51, 24, 51, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 80, 80, 240, 51, 51, 24, 24, 8, 1] 240
rigid atoms, others: [35, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 532
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043453 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043453
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043453/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043453
Building REAL250005043454
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043454'
/scratch/stefan/7916125/working/building/REAL250005043454 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043454

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043454/0 /scratch/stefan/7916125/working/building/REAL250005043454 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/562
`/scratch/stefan/7916125/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043454 none CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [19, 4, 19, 1, 4, 1, 1, 1, 1, 1, 8, 31, 31, 31, 35, 35, 35, 35, 35, 1, 1, 1, 1, 19, 19, 19, 19, 57, 1, 1, 8, 8, 31, 35, 2, 2, 2, 1, 1] 282
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 220
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043454 none CC(O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
282  conformations in input
total number of sets (complete confs): 282
using faster count positions algorithm for large data
unique positions, atoms: [94, 51, 94, 35, 51, 35, 35, 19, 35, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 94, 94, 94, 94, 282, 35, 35, 18, 18, 5, 1, 35, 35, 35, 35, 35] 282
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 663
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043454 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043454
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043454/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043454
Building REAL250005043455
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043455'
/scratch/stefan/7916125/working/building/REAL250005043455 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043455

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043455/0 /scratch/stefan/7916125/working/building/REAL250005043455 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/563
`/scratch/stefan/7916125/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1)

`REAL250005043455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043455 none C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 28, 45, 1, 1, 1, 1, 9, 43, 43, 43, 67, 67, 67, 67, 67, 2, 2, 2, 1, 1, 28, 28, 45, 45, 1, 1, 9, 9, 43, 67] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 10, 11, 12, 13, 33, 26, 27] set([6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37])
total number of confs: 338
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043455 none C[C@@H]1CN(C(=O)CCF)C[C@H]1CNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 67, 67, 67, 112, 112, 201, 201, 67, 23, 67, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 201, 201, 201, 201, 67, 67, 23, 23, 5, 1] 201
rigid atoms, others: [37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 769
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043455 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043455
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043455/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043455
Building REAL250005043456
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043456'
/scratch/stefan/7916125/working/building/REAL250005043456 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043456

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043456/0 /scratch/stefan/7916125/working/building/REAL250005043456 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/564
`/scratch/stefan/7916125/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043456 none C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [16, 5, 16, 16, 1, 5, 1, 1, 1, 1, 1, 7, 30, 30, 30, 36, 36, 36, 36, 36, 1, 1, 1, 1, 16, 16, 16, 48, 1, 1, 7, 7, 30, 36, 2, 2, 2, 1, 1] 243
rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 21, 22, 23, 38, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 198
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043456 none C[C@@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
243  conformations in input
total number of sets (complete confs): 243
using faster count positions algorithm for large data
unique positions, atoms: [81, 49, 81, 81, 36, 49, 36, 36, 17, 36, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 81, 81, 81, 243, 36, 36, 16, 16, 7, 1, 36, 36, 36, 36, 36] 243
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 567
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043456 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043456
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043456/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043456
Building REAL250005043457
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043457'
/scratch/stefan/7916125/working/building/REAL250005043457 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043457

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043457/0 /scratch/stefan/7916125/working/building/REAL250005043457 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/565
`/scratch/stefan/7916125/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043457 none C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
300  conformations in input
total number of sets (complete confs): 300
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 19, 1, 7, 1, 1, 1, 1, 1, 10, 41, 41, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 19, 19, 19, 57, 1, 1, 10, 10, 41, 50, 2, 2, 2, 1, 1] 300
rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 20, 21, 22, 23, 38, 28, 29] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 250
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043457 none C[C@H](O)C(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
300  conformations in input
total number of sets (complete confs): 300
using faster count positions algorithm for large data
unique positions, atoms: [100, 67, 100, 100, 50, 67, 50, 50, 22, 50, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 100, 100, 100, 300, 50, 50, 22, 22, 6, 1, 50, 50, 50, 50, 50] 300
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 680
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043457 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043457
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043457/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043457
Building REAL250005043458
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043458'
/scratch/stefan/7916125/working/building/REAL250005043458 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043458

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043458/0 /scratch/stefan/7916125/working/building/REAL250005043458 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/566
`/scratch/stefan/7916125/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1)

`REAL250005043458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043458 none CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [28, 27, 6, 1, 6, 1, 1, 1, 1, 1, 9, 42, 42, 42, 53, 53, 53, 53, 53, 1, 1, 1, 1, 28, 28, 28, 27, 28, 1, 1, 9, 9, 42, 53, 2, 2, 2, 1, 1] 106
rigid atoms, others: [3, 5, 6, 7, 8, 9, 19, 20, 21, 22, 38, 28, 29, 37] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 203
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043458 none CC=CC(=O)N1C[C@@H](CNC(=O)C2=CC(=O)[N-]O2)[C@H](C)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [106, 106, 90, 53, 90, 53, 53, 22, 53, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 106, 106, 106, 106, 106, 53, 53, 22, 22, 6, 1, 53, 53, 53, 53, 53] 106
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 344
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043458 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043458
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043458/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043458
Building REAL250005043459
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043459'
/scratch/stefan/7916125/working/building/REAL250005043459 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043459

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043459/0 /scratch/stefan/7916125/working/building/REAL250005043459 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/567
`/scratch/stefan/7916125/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043459 none COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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: [154, 131, 38, 38, 38, 8, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 154, 154, 154, 131, 131, 38, 8, 8, 1, 1, 20, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 544
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043459 none COCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 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, 143, 143, 143, 66, 20, 20, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 201, 201, 201, 201, 201, 143, 66, 66, 20, 20, 1, 20, 20, 20, 20, 20] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043459 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043459
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043459/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043459
Building REAL250005043460
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043460'
/scratch/stefan/7916125/working/building/REAL250005043460 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043460

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043460/0 /scratch/stefan/7916125/working/building/REAL250005043460 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/568
`/scratch/stefan/7916125/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043460 none CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [157, 138, 36, 36, 36, 9, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 17, 16, 16, 1, 1, 1, 1, 165, 165, 165, 165, 165, 138, 138, 36, 9, 9, 1, 1, 17, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 729
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043460 none CCCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 127, 127, 127, 53, 17, 17, 17, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 201, 201, 201, 201, 201, 197, 197, 127, 53, 53, 16, 17, 1, 16, 16, 17, 17, 17] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 788
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043460 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043460
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043460/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043460
Building REAL250005043461
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043461'
/scratch/stefan/7916125/working/building/REAL250005043461 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043461

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043461/0 /scratch/stefan/7916125/working/building/REAL250005043461 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/569
`/scratch/stefan/7916125/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043461 none CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [117, 39, 117, 39, 39, 9, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 39, 9, 9, 1, 1, 22, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 36, 37, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 38, 39, 40])
total number of confs: 469
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043461 none CC(C)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 174, 201, 174, 174, 87, 23, 23, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 22, 23, 23, 23, 201, 201, 201, 201, 201, 201, 201, 174, 87, 87, 22, 22, 1, 22, 23, 23, 23, 23] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043461 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043461
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043461/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043461
Building REAL250005043462
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043462'
/scratch/stefan/7916125/working/building/REAL250005043462 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043462

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043462/0 /scratch/stefan/7916125/working/building/REAL250005043462 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/570
`/scratch/stefan/7916125/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043462 none CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [130, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 130, 130, 130, 130, 130, 40, 9, 9, 1, 1, 26, 1, 1, 2, 2, 2] 201
rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 32, 35, 36, 37])
total number of confs: 508
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043462 none CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 163, 163, 163, 89, 26, 26, 26, 26, 9, 1, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 201, 201, 201, 201, 201, 163, 89, 89, 26, 26, 1, 26, 26, 26, 26, 26] 201
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37])
total number of confs: 763
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043462 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043462
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043462/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043462
Building REAL250005043463
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043463'
/scratch/stefan/7916125/working/building/REAL250005043463 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043463

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043463/0 /scratch/stefan/7916125/working/building/REAL250005043463 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/571
`/scratch/stefan/7916125/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043463 none CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 10, 1, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 1, 1, 40, 40, 40, 40, 10, 10, 1, 1, 36, 1, 1, 2, 2, 2] 109
rigid atoms, others: [4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 27, 28, 30, 31] set([0, 1, 2, 3, 33, 32, 10, 11, 12, 13, 14, 15, 16, 34, 21, 22, 23, 24, 25, 26, 29])
total number of confs: 160
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043463 none CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 36, 36, 36, 36, 9, 1, 9, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 109, 109, 109, 109, 95, 95, 36, 36, 1, 36, 36, 36, 36, 36] 109
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34])
total number of confs: 360
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043463 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043463
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043463/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043463
Building REAL250005043464
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043464'
/scratch/stefan/7916125/working/building/REAL250005043464 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043464

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043464/0 /scratch/stefan/7916125/working/building/REAL250005043464 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/572
`/scratch/stefan/7916125/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1)

`REAL250005043464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043464 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 8, 31, 31, 32, 120, 120, 2, 2, 2, 1, 1, 21, 1, 1, 8, 8, 32, 120, 120, 120, 120, 120] 173
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 355
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043464 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 21, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 67, 112, 112, 112, 173, 173, 21, 21, 21, 20, 20, 1, 21, 21, 67, 67, 112, 173, 173, 173, 173, 173] 173
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 573
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: REAL250005043464 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [122, 122, 122, 122, 122, 122, 169, 169, 175, 175, 175, 175, 175, 122, 57, 122, 12, 12, 1, 12, 1, 1, 1, 122, 122, 122, 122, 122, 175, 122, 122, 57, 57, 12, 1, 1, 1, 1, 1] 175
rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 573
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043464 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043464
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043464/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043464
Building REAL250005043465
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043465'
/scratch/stefan/7916125/working/building/REAL250005043465 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043465

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043465/0 /scratch/stefan/7916125/working/building/REAL250005043465 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/573
`/scratch/stefan/7916125/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O)

`REAL250005043465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043465 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 31, 32, 32, 32, 32, 1, 1, 1, 1, 10, 41, 41, 41, 74, 74, 2, 2, 2, 1, 1, 31, 1, 1, 10, 10, 41, 74, 74] 154
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35])
total number of confs: 262
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043465 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)C(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
154  conformations in input
total number of sets (complete confs): 154
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 32, 32, 31, 96, 150, 150, 150, 154, 154, 32, 32, 32, 32, 32, 1, 31, 31, 96, 96, 150, 154, 154] 154
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 509
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043465 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043465
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043465/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043465
Building REAL250005043466
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043466'
/scratch/stefan/7916125/working/building/REAL250005043466 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043466

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043466/0 /scratch/stefan/7916125/working/building/REAL250005043466 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/574
`/scratch/stefan/7916125/working/3D/574' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO)

`REAL250005043466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043466 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 28, 28, 1, 1, 1, 1, 9, 34, 34, 34, 74, 2, 2, 2, 1, 1, 27, 1, 1, 9, 9, 34, 76, 76, 228] 348
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 25, 26, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 555
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043466 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
348  conformations in input
total number of sets (complete confs): 348
using faster count positions algorithm for large data
unique positions, atoms: [28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 28, 27, 72, 113, 113, 113, 116, 28, 28, 28, 28, 28, 1, 27, 27, 72, 72, 113, 116, 116, 348] 348
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 27] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 754
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043466 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043466
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043466/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043466
Building REAL250005043467
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043467'
/scratch/stefan/7916125/working/building/REAL250005043467 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043467

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043467/0 /scratch/stefan/7916125/working/building/REAL250005043467 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/575
`/scratch/stefan/7916125/working/3D/575' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043467 none CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [129, 38, 125, 38, 38, 9, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 129, 129, 129, 129, 387, 38, 9, 9, 1, 1, 29, 1, 1, 2, 2, 2] 603
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 909
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043467 none CC(O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 199, 187, 187, 106, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 201, 201, 201, 201, 603, 187, 106, 106, 29, 29, 1, 29, 29, 29, 29, 29] 603
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 1310
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043467 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043467
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043467/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043467
Building REAL250005043468
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043468'
/scratch/stefan/7916125/working/building/REAL250005043468 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043468

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043468/0 /scratch/stefan/7916125/working/building/REAL250005043468 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/576
`/scratch/stefan/7916125/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043468 none CC(=O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [89, 42, 89, 42, 42, 9, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 89, 89, 89, 42, 9, 9, 1, 1, 29, 1, 1, 2, 2, 2] 181
rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 31, 34, 35, 36])
total number of confs: 302
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043468 none CC(=O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
181  conformations in input
total number of sets (complete confs): 181
using faster count positions algorithm for large data
unique positions, atoms: [181, 168, 181, 168, 168, 99, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 181, 181, 181, 168, 99, 99, 29, 29, 1, 29, 29, 29, 29, 29] 181
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 607
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043468 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043468
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043468/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043468
Building REAL250005043469
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043469'
/scratch/stefan/7916125/working/building/REAL250005043469 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043469

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043469/0 /scratch/stefan/7916125/working/building/REAL250005043469 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/577
`/scratch/stefan/7916125/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043469 none CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [104, 104, 39, 39, 39, 8, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 104, 104, 104, 104, 104, 39, 8, 8, 1, 1, 29, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 333
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043469 none CC=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 172, 172, 172, 94, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 201, 201, 201, 201, 201, 172, 94, 94, 29, 29, 1, 29, 29, 29, 29, 29] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 681
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043469 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043469
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043469/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043469
Building REAL250005043470
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043470'
/scratch/stefan/7916125/working/building/REAL250005043470 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043470

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043470/0 /scratch/stefan/7916125/working/building/REAL250005043470 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/578
`/scratch/stefan/7916125/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043470 none C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [132, 42, 132, 127, 42, 42, 10, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 132, 132, 132, 396, 42, 10, 10, 1, 1, 31, 1, 1, 2, 2, 2] 603
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 922
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043470 none C[C@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 187, 201, 201, 187, 187, 110, 31, 31, 31, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 201, 201, 201, 603, 187, 110, 110, 31, 31, 1, 31, 31, 31, 31, 31] 603
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 1313
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043470 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043470
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043470/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043470
Building REAL250005043471
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043471'
/scratch/stefan/7916125/working/building/REAL250005043471 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043471

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043471/0 /scratch/stefan/7916125/working/building/REAL250005043471 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/579
`/scratch/stefan/7916125/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043471 none C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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: [165, 129, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 1, 165, 165, 165, 129, 129, 35, 7, 7, 1, 1, 13, 1, 1, 2, 2, 2] 201
rigid atoms, others: [32, 34, 35, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043471 none C=CCC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 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, 127, 127, 127, 51, 14, 14, 14, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 201, 201, 201, 201, 201, 127, 51, 51, 13, 13, 1, 14, 14, 14, 14, 14] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 750
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043471 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043471
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043471/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043471
Building REAL250005043472
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043472'
/scratch/stefan/7916125/working/building/REAL250005043472 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043472

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043472/0 /scratch/stefan/7916125/working/building/REAL250005043472 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/580
`/scratch/stefan/7916125/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CC#N)

`REAL250005043472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043472 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 20, 20, 1, 1, 1, 1, 8, 34, 34, 34, 154, 154, 2, 2, 2, 1, 1, 19, 1, 1, 8, 8, 34, 154, 154] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35])
total number of confs: 582
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043472 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CC#N NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 19, 20, 19, 62, 146, 146, 146, 201, 201, 20, 20, 20, 20, 20, 1, 19, 19, 62, 62, 146, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 744
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043472 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043472
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043472/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043472
Building REAL250005043473
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043473'
/scratch/stefan/7916125/working/building/REAL250005043473 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043473

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043473/0 /scratch/stefan/7916125/working/building/REAL250005043473 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/581
`/scratch/stefan/7916125/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF)

`REAL250005043473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043473 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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, 6, 6, 14, 14, 14, 15, 15, 1, 1, 1, 1, 8, 33, 33, 33, 137, 164, 2, 2, 2, 1, 1, 14, 1, 1, 8, 8, 33, 137, 137, 164, 164] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 26, 27, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 674
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043473 none C[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1CNC(=O)CCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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']
dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 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: [15, 15, 15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 15, 15, 14, 50, 117, 117, 117, 201, 201, 15, 15, 15, 15, 15, 1, 14, 14, 50, 50, 117, 201, 201, 201, 201] 201
rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 28] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 777
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043473 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043473
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043473/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043473
Building REAL250005043474
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043474'
/scratch/stefan/7916125/working/building/REAL250005043474 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043474

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043474/0 /scratch/stefan/7916125/working/building/REAL250005043474 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/582
`/scratch/stefan/7916125/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043474 none C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
411  conformations in input
total number of sets (complete confs): 411
using faster count positions algorithm for large data
unique positions, atoms: [102, 37, 102, 101, 37, 37, 10, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 22, 22, 22, 1, 1, 1, 1, 102, 102, 102, 306, 37, 10, 10, 1, 1, 23, 1, 1, 2, 2, 2] 411
rigid atoms, others: [32, 34, 35, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 33, 36, 37, 38])
total number of confs: 717
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043474 none C[C@@H](O)C(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', '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: [5, 5, 7, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
411  conformations in input
total number of sets (complete confs): 411
using faster count positions algorithm for large data
unique positions, atoms: [137, 120, 137, 137, 120, 120, 70, 23, 23, 23, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 137, 137, 137, 411, 120, 70, 70, 22, 22, 1, 23, 23, 23, 23, 23] 411
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38])
total number of confs: 894
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043474 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043474
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043474/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043474
Building REAL250005043475
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043475'
/scratch/stefan/7916125/working/building/REAL250005043475 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043475

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043475/0 /scratch/stefan/7916125/working/building/REAL250005043475 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/583
`/scratch/stefan/7916125/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C)

`REAL250005043475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043475 none C=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [99, 43, 43, 43, 9, 1, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 99, 99, 99, 43, 9, 9, 1, 1, 31, 1, 1, 2, 2, 2] 182
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 28, 29, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35])
total number of confs: 340
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043475 none C=CC(=O)NC[C@@H]1CN(C(=O)C2=CC(=O)[N-]O2)C[C@H]1C NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [182, 182, 182, 182, 106, 31, 31, 31, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 182, 182, 182, 182, 106, 106, 31, 31, 1, 31, 31, 31, 31, 31] 182
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35])
total number of confs: 601
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043475 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043475
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043475/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043475
Building REAL250005043476
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043476'
/scratch/stefan/7916125/working/building/REAL250005043476 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043476

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043476/0 /scratch/stefan/7916125/working/building/REAL250005043476 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/584
`/scratch/stefan/7916125/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@]12CCC[C@H]1N(C(=O)C1=CC(=O)[N-]O1)CC2)

`REAL250005043476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043476 none CC(=O)NC[C@]12CCC[C@H]1N(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 1, 1, 30, 30, 30, 29, 9, 9, 1, 1, 1, 1, 1, 1, 32, 1, 1, 1, 1] 78
rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 37, 20, 21, 36, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27])
total number of confs: 132
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043476 none CC(=O)NC[C@]12CCC[C@H]1N(C(=O)C1=CC(=O)[N-]O1)CC2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 73, 32, 32, 32, 32, 32, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 32, 32, 78, 78, 78, 78, 73, 73, 32, 32, 32, 32, 32, 32, 1, 32, 32, 32, 32] 78
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 248
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043476 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043476
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043476/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043476
Building REAL250005043477
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043477'
/scratch/stefan/7916125/working/building/REAL250005043477 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043477

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043477/0 /scratch/stefan/7916125/working/building/REAL250005043477 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/585
`/scratch/stefan/7916125/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC[C@@]2(CNC(=O)C3=CC(=O)[N-]O3)CCC[C@@H]12)

`REAL250005043477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043477 none CC(=O)N1CC[C@@]2(CNC(=O)C3=CC(=O)[N-]O3)CCC[C@@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 10, 27, 27, 27, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 1, 10, 10, 27, 33, 1, 1, 1, 1, 1, 1] 43
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 38, 36, 33, 17, 18, 19, 20, 21, 25, 26, 27, 28, 37, 35] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 29, 30, 31])
total number of confs: 107
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043477 none CC(=O)N1CC[C@@]2(CNC(=O)C3=CC(=O)[N-]O3)CCC[C@@H]12 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 33, 43, 33, 33, 33, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 33, 15, 15, 6, 1, 33, 33, 33, 33, 33, 33] 43
rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 118
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043477 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043477
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043477/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043477
Building REAL250005043478
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043478'
/scratch/stefan/7916125/working/building/REAL250005043478 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043478

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043478/0 /scratch/stefan/7916125/working/building/REAL250005043478 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/586
`/scratch/stefan/7916125/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1)

`REAL250005043478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043478 none CCC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 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, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [116, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 1, 116, 116, 116, 116, 116, 37, 9, 9, 2, 2, 2, 1, 1, 29, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 6, 7, 8, 9, 10, 18, 19, 20, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34])
total number of confs: 468
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043478 none CCC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 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, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 158, 158, 158, 103, 29, 29, 29, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 201, 201, 201, 201, 201, 158, 103, 103, 29, 29, 29, 29, 29, 1, 29, 29, 29, 29] 201
rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 776
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043478 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043478
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043478/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043478
Building REAL250005043479
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043479'
/scratch/stefan/7916125/working/building/REAL250005043479 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043479

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043479/0 /scratch/stefan/7916125/working/building/REAL250005043479 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/587
`/scratch/stefan/7916125/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1)

`REAL250005043479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043479 none CC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [41, 41, 41, 9, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 1, 41, 41, 41, 41, 9, 9, 2, 2, 2, 1, 1, 35, 1, 1, 1, 1] 135
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31])
total number of confs: 164
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043479 none CC(=O)NCC1(C)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 108, 35, 35, 35, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 35, 35, 135, 135, 135, 135, 108, 108, 35, 35, 35, 35, 35, 1, 35, 35, 35, 35] 135
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 449
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043479 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043479
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043479/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043479
Building REAL250005043480
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043480'
/scratch/stefan/7916125/working/building/REAL250005043480 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043480

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043480/0 /scratch/stefan/7916125/working/building/REAL250005043480 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/588
`/scratch/stefan/7916125/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)CCO1)

`REAL250005043480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043480 none CC1(CNC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
525  conformations in input
total number of sets (complete confs): 525
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 10, 36, 36, 36, 88, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2, 10, 10, 36, 89, 89, 267, 1, 1, 38, 1, 1, 1, 1] 525
rigid atoms, others: [0, 1, 2, 35, 36, 33, 8, 9, 10, 34, 18, 19, 20, 30, 31] set([3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32])
total number of confs: 660
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043480 none CC1(CNC(=O)CO)CN(C(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
525  conformations in input
total number of sets (complete confs): 525
using faster count positions algorithm for large data
unique positions, atoms: [38, 38, 38, 124, 173, 173, 173, 175, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 124, 124, 173, 175, 175, 525, 38, 38, 1, 38, 38, 38, 38] 525
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1122
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043480 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043480
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043480/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043480
Building REAL250005043481
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043481'
/scratch/stefan/7916125/working/building/REAL250005043481 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043481

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043481/0 /scratch/stefan/7916125/working/building/REAL250005043481 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/589
`/scratch/stefan/7916125/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043481 none CCC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 47, 47, 47, 65, 65, 65, 65, 65, 1, 15, 15, 15, 14, 14, 1, 1, 1, 1, 2, 2, 2, 10, 10, 47, 64, 1, 1] 97
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 38, 20, 26, 27, 28, 29, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 220
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043481 none CCC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 96, 65, 96, 65, 65, 65, 65, 25, 65, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 65, 97, 97, 97, 97, 97, 65, 65, 65, 65, 65, 65, 65, 25, 25, 8, 1, 65, 65] 97
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 295
number of broken/clashed sets: 15
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043481 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043481
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043481/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043481
Building REAL250005043482
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043482'
/scratch/stefan/7916125/working/building/REAL250005043482 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043482

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043482/0 /scratch/stefan/7916125/working/building/REAL250005043482 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/590
`/scratch/stefan/7916125/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043482 none CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 10, 37, 37, 37, 49, 49, 49, 49, 49, 1, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 37, 49, 1, 1] 56
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 19, 23, 24, 25, 26, 35] set([0, 32, 2, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31])
total number of confs: 140
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043482 none CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 49, 56, 49, 49, 49, 49, 22, 49, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 49, 56, 56, 56, 49, 49, 49, 49, 49, 49, 49, 21, 21, 9, 1, 49, 49] 56
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 181
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043482 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043482
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043482/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043482
Building REAL250005043483
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043483'
/scratch/stefan/7916125/working/building/REAL250005043483 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043483

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043483/0 /scratch/stefan/7916125/working/building/REAL250005043483 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/591
`/scratch/stefan/7916125/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)CCO1)

`REAL250005043483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043483 none CC1(CNC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 10, 32, 32, 32, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 17, 1, 1, 1, 2, 2, 2, 10, 10, 32, 44, 1, 1, 17, 17, 51, 1, 1, 1, 1] 180
rigid atoms, others: [0, 1, 2, 34, 36, 35, 33, 12, 13, 14, 18, 19, 20, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32])
total number of confs: 227
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043483 none CC1(CNC(=O)C2=CC(=O)[N-]O2)CN(C(=O)CO)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
180  conformations in input
total number of sets (complete confs): 180
using faster count positions algorithm for large data
unique positions, atoms: [44, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 44, 44, 44, 59, 59, 60, 44, 44, 44, 44, 44, 44, 19, 19, 8, 1, 44, 44, 60, 60, 180, 44, 44, 44, 44] 180
rigid atoms, others: [4, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 375
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043483 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043483
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043483/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043483
Building REAL250005043484
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043484'
/scratch/stefan/7916125/working/building/REAL250005043484 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043484

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043484/0 /scratch/stefan/7916125/working/building/REAL250005043484 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/592
`/scratch/stefan/7916125/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043484 none C=CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [24, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 42, 42, 42, 55, 55, 55, 55, 55, 1, 24, 24, 24, 1, 1, 1, 1, 2, 2, 2, 10, 10, 42, 54, 1, 1] 75
rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 20, 24, 25, 26, 27, 36] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 202
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043484 none C=CC(=O)N1CCOC(C)(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 12, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 55, 75, 55, 55, 55, 55, 20, 55, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 55, 75, 75, 75, 55, 55, 55, 55, 55, 55, 55, 20, 20, 6, 1, 55, 55] 75
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 232
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043484 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043484
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043484/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043484
Building REAL250005043485
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043485'
/scratch/stefan/7916125/working/building/REAL250005043485 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043485

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043485/0 /scratch/stefan/7916125/working/building/REAL250005043485 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/593
`/scratch/stefan/7916125/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043485 none CCC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 1, 1] 9
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 34, 38, 37, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 35, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25])
total number of confs: 35
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043485 none CCC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 9, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8] 9
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 21
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043485 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043485
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043485/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043485
Building REAL250005043486
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043486'
/scratch/stefan/7916125/working/building/REAL250005043486 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043486

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043486/0 /scratch/stefan/7916125/working/building/REAL250005043486 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/594
`/scratch/stefan/7916125/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043486 none CC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 8, 1, 1] 11
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043486 none CC(=O)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 8, 11, 8, 8, 8, 8, 8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 8, 8] 11
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043486 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043486
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043486/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043486
Building REAL250005043487
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043487'
/scratch/stefan/7916125/working/building/REAL250005043487 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043487

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043487/0 /scratch/stefan/7916125/working/building/REAL250005043487 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/595
`/scratch/stefan/7916125/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043487 none O=C(CO)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 7, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 1, 1] 24
rigid atoms, others: [32, 1, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 34])
total number of confs: 53
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043487 none O=C(CO)N1CC2CC1CC(NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 8, 7, 7, 7, 7, 7, 7, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 8, 8, 24, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 7] 24
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 47
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043487 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043487
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043487/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043487
Building REAL250005043488
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043488'
/scratch/stefan/7916125/working/building/REAL250005043488 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043488

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043488/0 /scratch/stefan/7916125/working/building/REAL250005043488 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/596
`/scratch/stefan/7916125/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043488 none CCC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 1, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 1, 1] 80
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 38, 37, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043488 none CCC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 56, 56, 56, 31, 31, 31, 31, 31, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 31, 80, 80, 80, 80, 80, 56, 31, 31, 31, 31, 31, 31, 30, 30, 30, 1, 31, 31] 80
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 277
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043488 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043488
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043488/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043488
Building REAL250005043489
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043489'
/scratch/stefan/7916125/working/building/REAL250005043489 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043489

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043489/0 /scratch/stefan/7916125/working/building/REAL250005043489 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/597
`/scratch/stefan/7916125/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043489 none CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1] 8
rigid atoms, others: [32, 35, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23])
total number of confs: 20
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043489 none CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8] 8
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 16
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043489 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043489
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043489/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043489
Building REAL250005043490
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043490'
/scratch/stefan/7916125/working/building/REAL250005043490 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043490

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043490/0 /scratch/stefan/7916125/working/building/REAL250005043490 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/598
`/scratch/stefan/7916125/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043490 none O=C(CO)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 1, 9, 9, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1] 45
rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 76
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043490 none O=C(CO)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 15, 12, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 15, 15, 45, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12] 45
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 86
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043490 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043490
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043490/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043490
Building REAL250005043491
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043491'
/scratch/stefan/7916125/working/building/REAL250005043491 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043491

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043491/0 /scratch/stefan/7916125/working/building/REAL250005043491 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/599
`/scratch/stefan/7916125/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043491 none C=CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 1, 1] 57
rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 97
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043491 none C=CC(=O)NC1CC2CC(C1)N(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 57, 57, 29, 29, 29, 29, 29, 29, 29, 8, 1, 8, 1, 1, 1, 1, 1, 1, 29, 57, 57, 57, 57, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 29, 29] 57
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 135
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043491 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043491
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043491/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043491
Building REAL250005043492
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043492'
/scratch/stefan/7916125/working/building/REAL250005043492 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043492

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043492/0 /scratch/stefan/7916125/working/building/REAL250005043492 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/600
`/scratch/stefan/7916125/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043492 none CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 32, 32, 27, 27, 27, 27, 27, 5, 1, 1, 1, 1, 1, 1, 32] 58
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 133
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043492 none CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [58, 47, 47, 47, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 47, 32, 32, 32, 32, 32, 32, 1] 58
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 173
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043492 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043492
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043492/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043492
Building REAL250005043493
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043493'
/scratch/stefan/7916125/working/building/REAL250005043493 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043493

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043493/0 /scratch/stefan/7916125/working/building/REAL250005043493 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/601
`/scratch/stefan/7916125/working/3D/601' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043493 none CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 13, 13, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12] 15
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 33
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043493 none CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
15  conformations in input
total number of sets (complete confs): 15
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 12, 12, 13, 12, 12, 13, 13, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 13, 13, 13, 13, 12, 13, 1] 15
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 45
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043493 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043493
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043493/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043493
Building REAL250005043494
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043494'
/scratch/stefan/7916125/working/building/REAL250005043494 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043494

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043494/0 /scratch/stefan/7916125/working/building/REAL250005043494 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/602
`/scratch/stefan/7916125/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1)

`REAL250005043494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043494 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 5, 27, 27, 5, 1, 1, 1, 1, 1, 1, 20, 27, 27, 27, 27, 27] 69
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 36, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 95
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043494 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 1, 9, 1, 1, 1, 1, 1, 1, 33, 66, 66, 33, 22, 22, 22, 22, 22, 22, 1, 66, 66, 66, 66, 66] 66
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
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: REAL250005043494 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 57, 57, 70, 70, 70, 70, 70, 1, 1, 1, 12, 27, 27, 27, 27, 27, 27, 70, 1, 1, 1, 1, 1] 70
rigid atoms, others: [32, 1, 34, 35, 36, 33, 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])
total number of confs: 201
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043494 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043494
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043494/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043494
Building REAL250005043495
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043495'
/scratch/stefan/7916125/working/building/REAL250005043495 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043495

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043495/0 /scratch/stefan/7916125/working/building/REAL250005043495 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/603
`/scratch/stefan/7916125/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043495 none COCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [35, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 26, 25, 26, 26, 26, 35, 35, 35, 22, 22, 5, 1, 1, 1, 1, 1, 1, 26] 65
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 134
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043495 none COCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [65, 65, 41, 41, 41, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 41, 26, 26, 26, 26, 26, 26, 1] 65
rigid atoms, others: [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, 34, 35])
total number of confs: 230
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043495 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043495
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043495/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043495
Building REAL250005043496
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043496'
/scratch/stefan/7916125/working/building/REAL250005043496 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043496

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043496/0 /scratch/stefan/7916125/working/building/REAL250005043496 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/604
`/scratch/stefan/7916125/working/3D/604' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043496 none CCCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [45, 35, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 34, 53, 53, 53, 53, 53, 35, 35, 6, 1, 1, 1, 1, 1, 1, 34] 131
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 309
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043496 none CCCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [131, 129, 78, 78, 78, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 129, 129, 78, 34, 34, 34, 34, 34, 34, 1] 131
rigid atoms, others: [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, 37])
total number of confs: 450
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043496 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043496
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043496/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043496
Building REAL250005043497
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043497'
/scratch/stefan/7916125/working/building/REAL250005043497 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043497

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043497/0 /scratch/stefan/7916125/working/building/REAL250005043497 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/605
`/scratch/stefan/7916125/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043497 none CC(C)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [25, 5, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 31, 31, 31, 31, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 1, 30] 61
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043497 none CC(C)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 58, 61, 58, 58, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 58, 31, 31, 31, 31, 31, 31, 1] 61
rigid atoms, others: [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, 37])
total number of confs: 163
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043497 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043497
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043497/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043497
Building REAL250005043498
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043498'
/scratch/stefan/7916125/working/building/REAL250005043498 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043498

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043498/0 /scratch/stefan/7916125/working/building/REAL250005043498 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/606
`/scratch/stefan/7916125/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043498 none NC(=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 14, 14, 5, 1, 1, 1, 1, 1, 1, 17] 28
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 63
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043498 none NC(=O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 24, 28, 24, 24, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 1, 28, 28, 24, 17, 17, 17, 17, 17, 17, 1] 28
rigid atoms, others: [33, 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])
total number of confs: 71
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043498 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043498
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043498/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043498
Building REAL250005043499
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043499'
/scratch/stefan/7916125/working/building/REAL250005043499 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043499

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043499/0 /scratch/stefan/7916125/working/building/REAL250005043499 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/607
`/scratch/stefan/7916125/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043499 none C=CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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: [39, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 23, 22, 23, 23, 23, 39, 39, 39, 26, 26, 4, 1, 1, 1, 1, 1, 1, 23] 74
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 168
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043499 none C=CCC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 35, 35, 35, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 35, 23, 23, 23, 23, 23, 23, 1] 74
rigid atoms, others: [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, 34, 35])
total number of confs: 262
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043499 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043499
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043499/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043499
Building REAL250005043500
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043500'
/scratch/stefan/7916125/working/building/REAL250005043500 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043500

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043500/0 /scratch/stefan/7916125/working/building/REAL250005043500 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/608
`/scratch/stefan/7916125/working/3D/608' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043500 none O=C(CO)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 22, 23, 23, 23, 18, 18, 54, 5, 1, 1, 1, 1, 1, 1, 23] 96
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 155
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043500 none O=C(CO)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [32, 32, 32, 32, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 32, 32, 96, 32, 23, 23, 23, 23, 23, 23, 1] 96
rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 167
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043500 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043500
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043500/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043500
Building REAL250005043501
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043501'
/scratch/stefan/7916125/working/building/REAL250005043501 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043501

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043501/0 /scratch/stefan/7916125/working/building/REAL250005043501 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/609
`/scratch/stefan/7916125/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043501 none CC(O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [23, 5, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 19, 23, 23, 23, 23, 69, 5, 1, 1, 1, 1, 1, 1, 20] 126
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 177
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043501 none CC(O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [42, 31, 42, 31, 31, 20, 20, 20, 20, 19, 19, 20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 126, 31, 20, 20, 20, 20, 20, 20, 1] 126
rigid atoms, others: [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, 34, 35])
total number of confs: 257
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043501 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043501
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043501/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043501
Building REAL250005043502
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043502'
/scratch/stefan/7916125/working/building/REAL250005043502 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043502

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043502/0 /scratch/stefan/7916125/working/building/REAL250005043502 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/610
`/scratch/stefan/7916125/working/3D/610' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043502 none O=C(CCF)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 33, 58, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 30, 30, 30, 33, 33, 58, 58, 5, 1, 1, 1, 1, 1, 1, 30] 121
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 293
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043502 none O=C(CCF)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 121, 121, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 63, 30, 30, 30, 30, 30, 30, 1] 121
rigid atoms, others: [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, 34])
total number of confs: 428
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043502 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043502
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043502/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043502
Building REAL250005043503
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043503'
/scratch/stefan/7916125/working/building/REAL250005043503 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043503

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043503/0 /scratch/stefan/7916125/working/building/REAL250005043503 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/611
`/scratch/stefan/7916125/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043503 none C[C@@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [23, 5, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 23, 23, 23, 69, 5, 1, 1, 1, 1, 1, 1, 20] 126
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 177
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043503 none C[C@@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
126  conformations in input
total number of sets (complete confs): 126
using faster count positions algorithm for large data
unique positions, atoms: [42, 31, 42, 42, 31, 31, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 42, 42, 42, 126, 31, 20, 20, 20, 20, 20, 20, 1] 126
rigid atoms, others: [36, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 256
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043503 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043503
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043503/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043503
Building REAL250005043504
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043504'
/scratch/stefan/7916125/working/building/REAL250005043504 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043504

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043504/0 /scratch/stefan/7916125/working/building/REAL250005043504 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/612
`/scratch/stefan/7916125/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043504 none C[C@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [26, 5, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 26, 26, 26, 78, 5, 1, 1, 1, 1, 1, 1, 25] 156
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 199
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043504 none C[C@H](O)C(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
156  conformations in input
total number of sets (complete confs): 156
using faster count positions algorithm for large data
unique positions, atoms: [52, 40, 52, 52, 40, 40, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 52, 52, 52, 156, 40, 25, 25, 25, 25, 25, 25, 1] 156
rigid atoms, others: [36, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 314
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043504 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043504
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043504/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043504
Building REAL250005043505
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043505'
/scratch/stefan/7916125/working/building/REAL250005043505 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043505

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043505/0 /scratch/stefan/7916125/working/building/REAL250005043505 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/613
`/scratch/stefan/7916125/working/3D/613' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043505 none CC=CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 22] 45
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 83
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043505 none CC=CC(=O)N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 37, 22, 22, 22, 22, 22, 22, 1] 45
rigid atoms, others: [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, 34, 35])
total number of confs: 122
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043505 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043505
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043505/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043505
Building REAL250005043506
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043506'
/scratch/stefan/7916125/working/building/REAL250005043506 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043506

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043506/0 /scratch/stefan/7916125/working/building/REAL250005043506 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/614
`/scratch/stefan/7916125/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043506 none COCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [28, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 28, 28, 28, 16, 16, 1, 1, 1, 1, 5, 13, 1, 1] 40
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 92
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043506 none COCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [40, 39, 24, 13, 24, 13, 13, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 39, 39, 13, 13, 13, 13, 6, 1, 13, 13] 40
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 144
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043506 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043506
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043506/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043506
Building REAL250005043507
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043507'
/scratch/stefan/7916125/working/building/REAL250005043507 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043507

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043507/0 /scratch/stefan/7916125/working/building/REAL250005043507 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/615
`/scratch/stefan/7916125/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043507 none CCCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [23, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 28, 28, 28, 27, 27, 19, 19, 1, 1, 1, 1, 6, 14, 1, 1] 41
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 38, 37, 31] set([0, 1, 2, 35, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 155
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043507 none CCCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
41  conformations in input
total number of sets (complete confs): 41
using default count positions algorithm for smaller data
unique positions, atoms: [41, 40, 21, 14, 21, 14, 14, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 41, 41, 41, 41, 41, 40, 40, 14, 14, 14, 14, 7, 1, 14, 14] 41
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 152
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043507 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043507
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043507/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043507
Building REAL250005043508
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043508'
/scratch/stefan/7916125/working/building/REAL250005043508 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043508

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043508/0 /scratch/stefan/7916125/working/building/REAL250005043508 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/616
`/scratch/stefan/7916125/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043508 none CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 10, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 10, 1, 1] 16
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 38, 37, 31] set([0, 1, 2, 35, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 53
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043508 none CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [16, 14, 16, 10, 14, 10, 10, 10, 10, 10, 10, 10, 6, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 6, 1, 10, 10] 16
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 53
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043508 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043508
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043508/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043508
Building REAL250005043509
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043509'
/scratch/stefan/7916125/working/building/REAL250005043509 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043509

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043509/0 /scratch/stefan/7916125/working/building/REAL250005043509 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/617
`/scratch/stefan/7916125/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043509 none CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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]
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: [11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 12, 12, 12, 11, 11, 1, 1, 1, 1, 5, 13, 1, 1] 20
rigid atoms, others: [2, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 22, 28, 29, 30, 31] set([0, 1, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 62
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043509 none CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [20, 17, 13, 17, 13, 13, 13, 13, 13, 13, 13, 8, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 20, 20, 20, 20, 20, 13, 13, 13, 13, 8, 1, 13, 13] 20
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 65
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043509 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043509
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043509/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043509
Building REAL250005043510
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043510'
/scratch/stefan/7916125/working/building/REAL250005043510 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043510

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043510/0 /scratch/stefan/7916125/working/building/REAL250005043510 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/618
`/scratch/stefan/7916125/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043510 none CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
9  conformations in input
total number of sets (complete confs): 9
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 4, 4, 4, 1, 1, 1, 1, 5, 8, 1, 1] 9
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26, 27, 28, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 29, 30])
total number of confs: 27
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043510 none CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 9, 8, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 8, 8, 8, 8, 5, 1, 8, 8] 9
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 23
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043510 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043510
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043510/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043510
Building REAL250005043511
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043511'
/scratch/stefan/7916125/working/building/REAL250005043511 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043511

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043511/0 /scratch/stefan/7916125/working/building/REAL250005043511 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/619
`/scratch/stefan/7916125/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1)

`REAL250005043511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043511 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 5, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 11] 20
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 36, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 48
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043511 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 18, 20, 20, 20, 20, 20, 18, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 20] 20
rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 51
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: REAL250005043511 none O=C(N[C@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 20, 20, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 1] 20
rigid atoms, others: [1, 36, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 59
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043511 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043511
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043511/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043511
Building REAL250005043512
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043512'
/scratch/stefan/7916125/working/building/REAL250005043512 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043512

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043512/0 /scratch/stefan/7916125/working/building/REAL250005043512 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/620
`/scratch/stefan/7916125/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043512 none NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 15, 15, 1, 1, 1, 1, 5, 11, 1, 1] 27
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 26, 27, 28, 29] set([0, 1, 2, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31])
total number of confs: 60
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043512 none NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 24, 27, 11, 24, 11, 11, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 27, 27, 11, 11, 11, 11, 6, 1, 11, 11] 27
rigid atoms, others: [15, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 81
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043512 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043512
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043512/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043512
Building REAL250005043513
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043513'
/scratch/stefan/7916125/working/building/REAL250005043513 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043513

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043513/0 /scratch/stefan/7916125/working/building/REAL250005043513 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/621
`/scratch/stefan/7916125/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043513 none O=C(CO)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 6, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 12, 12, 36, 1, 1, 1, 1, 5, 10, 1, 1] 60
rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 26, 27, 28, 29] set([0, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 90
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043513 none O=C(CO)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [15, 10, 15, 20, 10, 10, 10, 10, 10, 10, 10, 6, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 20, 20, 60, 10, 10, 10, 10, 7, 1, 10, 10] 60
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 136
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043513 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043513
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043513/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043513
Building REAL250005043514
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043514'
/scratch/stefan/7916125/working/building/REAL250005043514 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043514

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043514/0 /scratch/stefan/7916125/working/building/REAL250005043514 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/622
`/scratch/stefan/7916125/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043514 none CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [13, 5, 13, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 13, 13, 13, 13, 39, 1, 1, 1, 1, 5, 8, 1, 1] 63
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 101
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043514 none CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [21, 12, 21, 8, 12, 8, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 63, 8, 8, 8, 8, 5, 1, 8, 8] 63
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 140
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043514 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043514
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043514/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043514
Building REAL250005043515
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043515'
/scratch/stefan/7916125/working/building/REAL250005043515 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043515

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043515/0 /scratch/stefan/7916125/working/building/REAL250005043515 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/623
`/scratch/stefan/7916125/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043515 none CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 6, 15, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 15, 15, 15, 1, 1, 1, 1, 5, 12, 1, 1] 24
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 27, 28, 29, 30] set([0, 1, 2, 4, 32, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31])
total number of confs: 57
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043515 none CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 21, 24, 12, 21, 12, 12, 12, 12, 12, 12, 12, 6, 12, 6, 1, 6, 1, 1, 1, 1, 1, 1, 12, 24, 24, 24, 12, 12, 12, 12, 7, 1, 12, 12] 24
rigid atoms, others: [32, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 73
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043515 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043515
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043515/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043515
Building REAL250005043516
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043516'
/scratch/stefan/7916125/working/building/REAL250005043516 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043516

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043516/0 /scratch/stefan/7916125/working/building/REAL250005043516 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/624
`/scratch/stefan/7916125/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043516 none CC=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 5, 12, 1, 1] 22
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 44
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043516 none CC=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 17, 12, 17, 12, 12, 12, 12, 12, 12, 12, 8, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 22, 22, 12, 12, 12, 12, 8, 1, 12, 12] 22
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 69
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043516 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043516
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043516/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043516
Building REAL250005043517
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043517'
/scratch/stefan/7916125/working/building/REAL250005043517 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043517

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043517/0 /scratch/stefan/7916125/working/building/REAL250005043517 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/625
`/scratch/stefan/7916125/working/3D/625' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043517 none C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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: [10, 6, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 10, 10, 10, 30, 1, 1, 1, 1, 5, 8, 1, 1] 60
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 75
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043517 none C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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, 12, 20, 20, 8, 12, 8, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 60, 8, 8, 8, 8, 5, 1, 8, 8] 60
rigid atoms, others: [34, 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, 35, 36])
total number of confs: 134
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043517 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043517
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043517/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043517
Building REAL250005043518
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043518'
/scratch/stefan/7916125/working/building/REAL250005043518 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043518

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043518/0 /scratch/stefan/7916125/working/building/REAL250005043518 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/626
`/scratch/stefan/7916125/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043518 none C=CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [31, 22, 7, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 31, 31, 31, 22, 22, 1, 1, 1, 1, 5, 14, 1, 1] 45
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 132
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043518 none C=CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 27, 14, 27, 14, 14, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 45, 45, 45, 45, 45, 14, 14, 14, 14, 7, 1, 14, 14] 45
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 159
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043518 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043518
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043518/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043518
Building REAL250005043519
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043519'
/scratch/stefan/7916125/working/building/REAL250005043519 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043519

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043519/0 /scratch/stefan/7916125/working/building/REAL250005043519 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/627
`/scratch/stefan/7916125/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043519 none N#CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 19, 19, 1, 1, 1, 1, 6, 13, 1, 1] 32
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 26, 27, 28, 29] set([0, 1, 2, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31])
total number of confs: 81
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043519 none N#CCC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
32  conformations in input
total number of sets (complete confs): 32
using default count positions algorithm for smaller data
unique positions, atoms: [32, 32, 21, 13, 21, 13, 13, 13, 13, 13, 13, 13, 7, 13, 8, 1, 8, 1, 1, 1, 1, 1, 1, 13, 32, 32, 13, 13, 13, 13, 8, 1, 13, 13] 32
rigid atoms, others: [15, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 111
number of broken/clashed sets: 11
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043519 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043519
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043519/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043519
Building REAL250005043520
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043520'
/scratch/stefan/7916125/working/building/REAL250005043520 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043520

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043520/0 /scratch/stefan/7916125/working/building/REAL250005043520 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/628
`/scratch/stefan/7916125/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043520 none O=C(CCF)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 13, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 1, 13, 13, 22, 22, 1, 1, 1, 1, 5, 11, 1, 1] 40
rigid atoms, others: [1, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 33, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27])
total number of confs: 108
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043520 none O=C(CCF)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
40  conformations in input
total number of sets (complete confs): 40
using default count positions algorithm for smaller data
unique positions, atoms: [17, 11, 17, 40, 40, 11, 11, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 40, 40, 40, 40, 11, 11, 11, 11, 6, 1, 11, 11] 40
rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 147
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043520 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043520
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043520/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043520
Building REAL250005043521
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043521'
/scratch/stefan/7916125/working/building/REAL250005043521 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043521

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043521/0 /scratch/stefan/7916125/working/building/REAL250005043521 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/629
`/scratch/stefan/7916125/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043521 none C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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: [10, 3, 10, 10, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 10, 10, 10, 30, 1, 1, 1, 1, 5, 8, 1, 1] 60
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 81
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043521 none C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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, 11, 20, 20, 8, 11, 8, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 60, 8, 8, 8, 8, 5, 1, 8, 8] 60
rigid atoms, others: [34, 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, 35, 36])
total number of confs: 136
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043521 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043521
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043521/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043521
Building REAL250005043522
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043522'
/scratch/stefan/7916125/working/building/REAL250005043522 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043522

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043522/0 /scratch/stefan/7916125/working/building/REAL250005043522 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/630
`/scratch/stefan/7916125/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043522 none C=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 8, 9, 9, 1, 1, 1, 1, 5, 9, 1, 1] 14
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 26, 27, 28, 29] set([0, 1, 3, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 40
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043522 none C=CC(=O)N1[C@@H]2CC[C@H]1[C@@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
14  conformations in input
total number of sets (complete confs): 14
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 9, 14, 9, 9, 9, 9, 9, 9, 9, 6, 9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 14, 14, 14, 9, 9, 9, 9, 6, 1, 9, 9] 14
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 37
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043522 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043522
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043522/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043522
Building REAL250005043523
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043523'
/scratch/stefan/7916125/working/building/REAL250005043523 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043523

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043523/0 /scratch/stefan/7916125/working/building/REAL250005043523 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/631
`/scratch/stefan/7916125/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043523 none CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [32, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 33, 33, 32, 32, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 32] 69
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 35, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 152
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043523 none CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 51, 51, 51, 33, 33, 33, 33, 33, 33, 33, 33, 32, 32, 9, 1, 9, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 51, 33, 33, 33, 33, 33, 33, 1] 69
rigid atoms, others: [35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 222
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043523 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043523
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043523/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043523
Building REAL250005043524
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043524'
/scratch/stefan/7916125/working/building/REAL250005043524 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043524

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043524/0 /scratch/stefan/7916125/working/building/REAL250005043524 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/632
`/scratch/stefan/7916125/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043524 none CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 17] 19
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25])
total number of confs: 40
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043524 none CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 17, 17, 17, 17, 17, 17, 1] 19
rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 40
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043524 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043524
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043524/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043524
Building REAL250005043525
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043525'
/scratch/stefan/7916125/working/building/REAL250005043525 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043525

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043525/0 /scratch/stefan/7916125/working/building/REAL250005043525 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/633
`/scratch/stefan/7916125/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1)

`REAL250005043525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043525 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 6, 30, 30, 6, 1, 1, 1, 1, 1, 1, 28, 30, 30, 30, 30, 30] 83
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 36, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043525 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 54, 83, 83, 54, 28, 28, 28, 28, 28, 28, 1, 83, 83, 83, 83, 83] 83
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36])
total number of confs: 233
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043525 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 70, 70, 83, 83, 83, 83, 83, 1, 1, 1, 12, 30, 30, 30, 30, 30, 30, 83, 1, 1, 1, 1, 1] 83
rigid atoms, others: [32, 1, 34, 35, 36, 33, 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])
total number of confs: 222
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043525 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043525
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043525/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043525
Building REAL250005043526
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043526'
/scratch/stefan/7916125/working/building/REAL250005043526 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043526

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043526/0 /scratch/stefan/7916125/working/building/REAL250005043526 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/634
`/scratch/stefan/7916125/working/3D/634' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043526 none COCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [65, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 31, 31, 31, 31, 65, 65, 65, 40, 40, 6, 1, 1, 1, 1, 1, 1, 30] 128
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 217
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043526 none COCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 127, 76, 76, 76, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 128, 128, 128, 127, 127, 76, 31, 31, 31, 31, 31, 31, 1] 128
rigid atoms, others: [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, 34, 35])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043526 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043526
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043526/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043526
Building REAL250005043527
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043527'
/scratch/stefan/7916125/working/building/REAL250005043527 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043527

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043527/0 /scratch/stefan/7916125/working/building/REAL250005043527 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/635
`/scratch/stefan/7916125/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043527 none CCCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [47, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 30, 31, 31, 31, 56, 56, 56, 56, 56, 34, 34, 6, 1, 1, 1, 1, 1, 1, 30] 144
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 335
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043527 none CCCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 141, 86, 86, 86, 31, 31, 31, 31, 31, 31, 31, 31, 30, 30, 9, 1, 9, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 141, 141, 86, 31, 31, 31, 31, 31, 31, 1] 144
rigid atoms, others: [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, 37])
total number of confs: 507
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043527 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043527
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043527/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043527
Building REAL250005043528
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043528'
/scratch/stefan/7916125/working/building/REAL250005043528 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043528

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043528/0 /scratch/stefan/7916125/working/building/REAL250005043528 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/636
`/scratch/stefan/7916125/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043528 none CC(C)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [25, 6, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 30, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 31] 71
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 37] set([0, 1, 2, 3, 4, 38, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 129
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043528 none CC(C)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 57, 71, 57, 57, 31, 31, 31, 31, 30, 30, 31, 31, 31, 31, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 57, 31, 31, 31, 31, 31, 31, 1] 71
rigid atoms, others: [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, 37])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043528 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043528
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043528/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043528
Building REAL250005043529
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043529'
/scratch/stefan/7916125/working/building/REAL250005043529 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043529

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043529/0 /scratch/stefan/7916125/working/building/REAL250005043529 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/637
`/scratch/stefan/7916125/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043529 none NC(=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [22, 6, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 22, 22, 6, 1, 1, 1, 1, 1, 1, 18] 37
rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 85
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043529 none NC(=O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
37  conformations in input
total number of sets (complete confs): 37
using default count positions algorithm for smaller data
unique positions, atoms: [37, 31, 37, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 1, 37, 37, 31, 18, 18, 18, 18, 18, 18, 1] 37
rigid atoms, others: [33, 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])
total number of confs: 100
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043529 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043529
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043529/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043529
Building REAL250005043530
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043530'
/scratch/stefan/7916125/working/building/REAL250005043530 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043530

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043530/0 /scratch/stefan/7916125/working/building/REAL250005043530 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/638
`/scratch/stefan/7916125/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043530 none C=CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [60, 34, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 24, 60, 60, 60, 34, 34, 6, 1, 1, 1, 1, 1, 1, 25] 102
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 230
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043530 none C=CCC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [102, 102, 53, 53, 53, 25, 25, 25, 25, 24, 24, 25, 25, 25, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 102, 53, 25, 25, 25, 25, 25, 25, 1] 102
rigid atoms, others: [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, 34, 35])
total number of confs: 376
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043530 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043530
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043530/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043530
Building REAL250005043531
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043531'
/scratch/stefan/7916125/working/building/REAL250005043531 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043531

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043531/0 /scratch/stefan/7916125/working/building/REAL250005043531 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/639
`/scratch/stefan/7916125/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043531 none O=C(CO)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 33, 31, 31, 93, 6, 1, 1, 1, 1, 1, 1, 33] 177
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043531 none O=C(CO)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 52, 59, 33, 33, 33, 32, 32, 32, 32, 33, 33, 33, 9, 1, 9, 1, 1, 1, 1, 1, 1, 59, 59, 177, 52, 33, 32, 33, 32, 33, 33, 1] 177
rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 342
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043531 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043531
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043531/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043531
Building REAL250005043532
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043532'
/scratch/stefan/7916125/working/building/REAL250005043532 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043532

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043532/0 /scratch/stefan/7916125/working/building/REAL250005043532 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/640
`/scratch/stefan/7916125/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043532 none CC(O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 36, 36, 35, 35, 36, 36, 36, 36, 108, 6, 1, 1, 1, 1, 1, 1, 35] 270
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 276
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043532 none CC(O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [90, 69, 90, 69, 69, 36, 36, 36, 35, 35, 35, 35, 36, 35, 35, 9, 1, 9, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 270, 69, 36, 36, 35, 36, 36, 36, 1] 270
rigid atoms, others: [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, 34, 35])
total number of confs: 555
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043532 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043532
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043532/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043532
Building REAL250005043533
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043533'
/scratch/stefan/7916125/working/building/REAL250005043533 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043533

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043533/0 /scratch/stefan/7916125/working/building/REAL250005043533 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/641
`/scratch/stefan/7916125/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043533 none O=C(CCF)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 6, 37, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 26, 27, 27, 27, 37, 37, 68, 68, 6, 1, 1, 1, 1, 1, 1, 26] 138
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 35, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28])
total number of confs: 334
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043533 none O=C(CCF)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 138, 138, 27, 27, 27, 27, 27, 27, 27, 27, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 71, 27, 27, 27, 27, 27, 27, 1] 138
rigid atoms, others: [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, 34])
total number of confs: 479
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043533 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043533
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043533/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043533
Building REAL250005043534
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043534'
/scratch/stefan/7916125/working/building/REAL250005043534 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043534

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043534/0 /scratch/stefan/7916125/working/building/REAL250005043534 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/642
`/scratch/stefan/7916125/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043534 none C[C@@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
264  conformations in input
total number of sets (complete confs): 264
using faster count positions algorithm for large data
unique positions, atoms: [37, 6, 37, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 35, 35, 35, 35, 37, 37, 37, 111, 6, 1, 1, 1, 1, 1, 1, 34] 264
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 280
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043534 none C[C@@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
264  conformations in input
total number of sets (complete confs): 264
using faster count positions algorithm for large data
unique positions, atoms: [88, 67, 88, 88, 67, 67, 35, 34, 34, 35, 35, 35, 35, 34, 34, 34, 9, 1, 9, 1, 1, 1, 1, 1, 1, 88, 88, 88, 264, 67, 35, 35, 35, 35, 34, 35, 1] 264
rigid atoms, others: [36, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 545
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043534 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043534
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043534/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043534
Building REAL250005043535
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043535'
/scratch/stefan/7916125/working/building/REAL250005043535 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043535

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043535/0 /scratch/stefan/7916125/working/building/REAL250005043535 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/643
`/scratch/stefan/7916125/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043535 none C[C@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [36, 6, 36, 36, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 35, 36, 36, 36, 36, 36, 108, 6, 1, 1, 1, 1, 1, 1, 35] 255
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 275
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043535 none C[C@H](O)C(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [85, 65, 85, 85, 65, 65, 36, 35, 36, 36, 36, 36, 36, 35, 35, 35, 9, 1, 9, 1, 1, 1, 1, 1, 1, 85, 85, 85, 255, 65, 36, 36, 36, 36, 36, 36, 1] 255
rigid atoms, others: [36, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 525
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043535 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043535
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043535/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043535
Building REAL250005043536
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043536'
/scratch/stefan/7916125/working/building/REAL250005043536 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043536

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043536/0 /scratch/stefan/7916125/working/building/REAL250005043536 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/644
`/scratch/stefan/7916125/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1)

`REAL250005043536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043536 none CC=CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 22] 45
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36])
total number of confs: 70
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043536 none CC=CC(=O)N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 37, 37, 37, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 37, 22, 22, 22, 22, 22, 22, 1] 45
rigid atoms, others: [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, 34, 35])
total number of confs: 123
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043536 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043536
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043536/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043536
Building REAL250005043537
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043537'
/scratch/stefan/7916125/working/building/REAL250005043537 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043537

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043537/0 /scratch/stefan/7916125/working/building/REAL250005043537 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/645
`/scratch/stefan/7916125/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043537 none COCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [34, 16, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 34, 34, 34, 16, 16, 1, 1, 1, 1, 6, 13, 1, 1] 43
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 108
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043537 none COCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
43  conformations in input
total number of sets (complete confs): 43
using default count positions algorithm for smaller data
unique positions, atoms: [43, 40, 23, 13, 23, 13, 13, 13, 13, 13, 13, 13, 5, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 43, 43, 43, 40, 40, 13, 13, 13, 13, 6, 1, 13, 13] 43
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 151
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043537 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043537
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043537/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043537
Building REAL250005043538
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043538'
/scratch/stefan/7916125/working/building/REAL250005043538 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043538

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043538/0 /scratch/stefan/7916125/working/building/REAL250005043538 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/646
`/scratch/stefan/7916125/working/3D/646' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043538 none CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [28, 23, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 1, 30, 30, 30, 30, 30, 23, 23, 1, 1, 1, 1, 6, 20, 1, 1] 57
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 38, 37, 31] set([0, 1, 2, 35, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 164
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043538 none CCCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 57, 34, 20, 34, 20, 20, 20, 20, 20, 20, 20, 9, 20, 9, 1, 9, 1, 1, 1, 1, 1, 1, 20, 57, 57, 57, 57, 57, 57, 57, 20, 20, 20, 20, 9, 1, 20, 20] 57
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 198
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043538 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043538
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043538/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043538
Building REAL250005043539
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043539'
/scratch/stefan/7916125/working/building/REAL250005043539 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043539

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043539/0 /scratch/stefan/7916125/working/building/REAL250005043539 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/647
`/scratch/stefan/7916125/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043539 none CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [10, 6, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 6, 14, 1, 1] 22
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 38, 37, 31] set([0, 1, 2, 35, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 61
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043539 none CC(C)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 14, 22, 14, 14, 14, 14, 14, 14, 14, 7, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 14, 7, 1, 14, 14] 22
rigid atoms, others: [36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 65
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043539 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043539
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043539/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043539
Building REAL250005043540
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043540'
/scratch/stefan/7916125/working/building/REAL250005043540 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043540

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043540/0 /scratch/stefan/7916125/working/building/REAL250005043540 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/648
`/scratch/stefan/7916125/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043540 none CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 17, 1, 12, 12, 12, 11, 11, 1, 1, 1, 1, 6, 17, 1, 1] 26
rigid atoms, others: [2, 34, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 22, 28, 29, 30, 31] set([0, 1, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27])
total number of confs: 69
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043540 none CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
26  conformations in input
total number of sets (complete confs): 26
using default count positions algorithm for smaller data
unique positions, atoms: [26, 23, 17, 23, 17, 17, 17, 17, 17, 17, 17, 9, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 26, 26, 26, 26, 26, 17, 17, 17, 17, 9, 1, 17, 17] 26
rigid atoms, others: [33, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 81
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043540 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043540
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043540/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043540
Building REAL250005043541
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043541'
/scratch/stefan/7916125/working/building/REAL250005043541 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043541

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043541/0 /scratch/stefan/7916125/working/building/REAL250005043541 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/649
`/scratch/stefan/7916125/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043541 none CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 5, 5, 5, 1, 1, 1, 1, 5, 8, 1, 1] 12
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 25, 26, 27, 28, 31] set([0, 2, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 29, 30])
total number of confs: 31
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043541 none CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 8, 12, 8, 8, 8, 8, 8, 8, 8, 5, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 8, 8, 8, 8, 6, 1, 8, 8] 12
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043541 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043541
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043541/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043541
Building REAL250005043542
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043542'
/scratch/stefan/7916125/working/building/REAL250005043542 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043542

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043542/0 /scratch/stefan/7916125/working/building/REAL250005043542 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/650
`/scratch/stefan/7916125/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1)

`REAL250005043542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043542 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 5, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 11] 24
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30] set([0, 1, 34, 35, 36, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31])
total number of confs: 53
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043542 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 1, 8, 1, 1, 1, 20, 24, 24, 24, 24, 24, 20, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 24] 24
rigid atoms, others: [32, 33, 34, 35, 13, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36])
total number of confs: 58
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043542 none O=C(N[C@@H]1C[C@H]2CC[C@@H]1N2C(=O)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [7, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 24, 24, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 1] 24
rigid atoms, others: [1, 36, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 77
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043542 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043542
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043542/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043542
Building REAL250005043543
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043543'
/scratch/stefan/7916125/working/building/REAL250005043543 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043543

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043543/0 /scratch/stefan/7916125/working/building/REAL250005043543 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/651
`/scratch/stefan/7916125/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043543 none NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [14, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 14, 14, 1, 1, 1, 1, 5, 10, 1, 1] 23
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 26, 27, 28, 29] set([0, 1, 2, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31])
total number of confs: 55
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043543 none NC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 18, 23, 10, 18, 10, 10, 10, 10, 10, 10, 10, 5, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 23, 23, 10, 10, 10, 10, 6, 1, 10, 10] 23
rigid atoms, others: [15, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 75
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043543 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043543
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043543/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043543
Building REAL250005043544
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043544'
/scratch/stefan/7916125/working/building/REAL250005043544 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043544

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043544/0 /scratch/stefan/7916125/working/building/REAL250005043544 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/652
`/scratch/stefan/7916125/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043544 none O=C(CO)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 1, 8, 8, 24, 1, 1, 1, 1, 6, 11, 1, 1] 54
rigid atoms, others: [32, 1, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 26, 27, 28, 29] set([0, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 73
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043544 none O=C(CO)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [17, 11, 17, 18, 11, 11, 11, 11, 11, 11, 11, 6, 11, 6, 1, 6, 1, 1, 1, 1, 1, 1, 11, 18, 18, 54, 11, 11, 11, 11, 6, 1, 11, 11] 54
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 109
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043544 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043544
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043544/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043544
Building REAL250005043545
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043545'
/scratch/stefan/7916125/working/building/REAL250005043545 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043545

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043545/0 /scratch/stefan/7916125/working/building/REAL250005043545 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/653
`/scratch/stefan/7916125/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043545 none CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 21, 21, 21, 21, 63, 1, 1, 1, 1, 6, 16, 1, 1] 123
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 159
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043545 none CC(O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [41, 28, 41, 16, 28, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 41, 41, 41, 41, 123, 16, 16, 16, 16, 9, 1, 16, 16] 123
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 269
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043545 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043545
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043545/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043545
Building REAL250005043546
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043546'
/scratch/stefan/7916125/working/building/REAL250005043546 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043546

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043546/0 /scratch/stefan/7916125/working/building/REAL250005043546 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/654
`/scratch/stefan/7916125/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043546 none CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [11, 4, 11, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 12, 12, 12, 1, 1, 1, 1, 5, 9, 1, 1] 21
rigid atoms, others: [33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 27, 28, 29, 30] set([0, 1, 2, 4, 32, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31])
total number of confs: 49
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043546 none CC(=O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
21  conformations in input
total number of sets (complete confs): 21
using default count positions algorithm for smaller data
unique positions, atoms: [21, 13, 21, 9, 13, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 9, 9, 9, 9, 5, 1, 9, 9] 21
rigid atoms, others: [32, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043546 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043546
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043546/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043546
Building REAL250005043547
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043547'
/scratch/stefan/7916125/working/building/REAL250005043547 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043547

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043547/0 /scratch/stefan/7916125/working/building/REAL250005043547 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/655
`/scratch/stefan/7916125/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043547 none CC=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 1, 16, 16, 16, 15, 15, 1, 1, 1, 1, 6, 15, 1, 1] 30
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 73
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043547 none CC=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
30  conformations in input
total number of sets (complete confs): 30
using default count positions algorithm for smaller data
unique positions, atoms: [30, 30, 26, 15, 26, 15, 15, 15, 15, 15, 15, 15, 6, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 30, 30, 30, 30, 30, 15, 15, 15, 15, 6, 1, 15, 15] 30
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 89
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043547 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043547
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043547/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043547
Building REAL250005043548
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043548'
/scratch/stefan/7916125/working/building/REAL250005043548 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043548

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043548/0 /scratch/stefan/7916125/working/building/REAL250005043548 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/656
`/scratch/stefan/7916125/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043548 none C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [21, 6, 21, 21, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 1, 21, 21, 21, 63, 1, 1, 1, 1, 6, 16, 1, 1] 123
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 159
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043548 none C[C@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
123  conformations in input
total number of sets (complete confs): 123
using faster count positions algorithm for large data
unique positions, atoms: [41, 28, 41, 41, 16, 28, 16, 16, 16, 16, 16, 16, 16, 8, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 41, 41, 41, 123, 16, 16, 16, 16, 8, 1, 16, 16] 123
rigid atoms, others: [34, 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, 35, 36])
total number of confs: 267
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043548 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043548
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043548/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043548
Building REAL250005043549
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043549'
/scratch/stefan/7916125/working/building/REAL250005043549 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043549

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043549/0 /scratch/stefan/7916125/working/building/REAL250005043549 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/657
`/scratch/stefan/7916125/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043549 none C=CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [33, 16, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 1, 33, 33, 33, 16, 16, 1, 1, 1, 1, 6, 14, 1, 1] 46
rigid atoms, others: [32, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 23, 29, 30, 31] set([0, 1, 2, 4, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28])
total number of confs: 137
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043549 none C=CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
46  conformations in input
total number of sets (complete confs): 46
using default count positions algorithm for smaller data
unique positions, atoms: [46, 46, 30, 14, 30, 14, 14, 14, 14, 14, 14, 14, 7, 14, 7, 1, 7, 1, 1, 1, 1, 1, 1, 14, 46, 46, 46, 46, 46, 14, 14, 14, 14, 7, 1, 14, 14] 46
rigid atoms, others: [34, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 161
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043549 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043549
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043549/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043549
Building REAL250005043550
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043550'
/scratch/stefan/7916125/working/building/REAL250005043550 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043550

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043550/0 /scratch/stefan/7916125/working/building/REAL250005043550 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/658
`/scratch/stefan/7916125/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043550 none N#CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 1, 12, 12, 1, 1, 1, 1, 6, 13, 1, 1] 27
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 26, 27, 28, 29] set([0, 1, 2, 4, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 30, 31])
total number of confs: 64
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043550 none N#CCC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 27, 16, 13, 16, 13, 13, 13, 13, 13, 13, 13, 6, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 27, 27, 13, 13, 13, 13, 6, 1, 13, 13] 27
rigid atoms, others: [15, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043550 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043550
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043550/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043550
Building REAL250005043551
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043551'
/scratch/stefan/7916125/working/building/REAL250005043551 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043551

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043551/0 /scratch/stefan/7916125/working/building/REAL250005043551 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/659
`/scratch/stefan/7916125/working/3D/659' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043551 none O=C(CCF)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [5, 1, 5, 17, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 1, 17, 17, 29, 29, 1, 1, 1, 1, 6, 19, 1, 1] 58
rigid atoms, others: [1, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 33, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27])
total number of confs: 151
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043551 none O=C(CCF)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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]
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: [33, 19, 33, 58, 58, 19, 19, 19, 19, 19, 19, 19, 7, 19, 7, 1, 7, 1, 1, 1, 1, 1, 1, 19, 58, 58, 58, 58, 19, 19, 19, 19, 8, 1, 19, 19] 58
rigid atoms, others: [33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 216
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043551 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043551
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043551/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043551
Building REAL250005043552
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043552'
/scratch/stefan/7916125/working/building/REAL250005043552 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043552

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043552/0 /scratch/stefan/7916125/working/building/REAL250005043552 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/660
`/scratch/stefan/7916125/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043552 none C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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: [10, 4, 10, 10, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 9, 1, 10, 10, 10, 30, 1, 1, 1, 1, 6, 9, 1, 1] 60
rigid atoms, others: [32, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28])
total number of confs: 81
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043552 none C[C@@H](O)C(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7]
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, 3, 7, 3, 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, 14, 20, 20, 9, 14, 9, 9, 9, 9, 9, 9, 9, 5, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 60, 9, 9, 9, 9, 5, 1, 9, 9] 60
rigid atoms, others: [34, 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, 35, 36])
total number of confs: 129
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043552 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043552
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043552/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043552
Building REAL250005043553
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043553'
/scratch/stefan/7916125/working/building/REAL250005043553 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043553

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043553/0 /scratch/stefan/7916125/working/building/REAL250005043553 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/661
`/scratch/stefan/7916125/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043553 none C=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 1, 10, 10, 10, 1, 1, 1, 1, 6, 12, 1, 1] 19
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 26, 27, 28, 29] set([0, 1, 3, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 30, 31])
total number of confs: 47
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043553 none C=CC(=O)N1[C@@H]2CC[C@H]1[C@H](NC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 7, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 12, 19, 12, 12, 12, 12, 12, 12, 12, 5, 12, 5, 1, 5, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 12, 12, 12, 12, 6, 1, 12, 12] 19
rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043553 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043553
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043553/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043553
Building REAL250005043554
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043554'
/scratch/stefan/7916125/working/building/REAL250005043554 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043554

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043554/0 /scratch/stefan/7916125/working/building/REAL250005043554 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/662
`/scratch/stefan/7916125/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043554 none CCC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 28, 28, 28, 28, 28, 1, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 28, 1, 1] 57
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 21, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27])
total number of confs: 103
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043554 none CCC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 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, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
57  conformations in input
total number of sets (complete confs): 57
using faster count positions algorithm for large data
unique positions, atoms: [57, 42, 42, 42, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 57, 57, 57, 57, 57, 42, 28, 28, 28, 28, 28, 28, 28, 28, 1, 28, 28] 57
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 190
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043554 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043554
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043554/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043554
Building REAL250005043555
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043555'
/scratch/stefan/7916125/working/building/REAL250005043555 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043555

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043555/0 /scratch/stefan/7916125/working/building/REAL250005043555 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/663
`/scratch/stefan/7916125/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043555 none CC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 1, 1] 18
rigid atoms, others: [32, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 35, 20, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 33, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24])
total number of confs: 27
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043555 none CC(=O)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 10, 10, 10, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 10, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 1, 10, 10] 18
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 51
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043555 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043555
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043555/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043555
Building REAL250005043556
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043556'
/scratch/stefan/7916125/working/building/REAL250005043556 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043556

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043556/0 /scratch/stefan/7916125/working/building/REAL250005043556 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/664
`/scratch/stefan/7916125/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043556 none O=C(CO)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 21, 1, 12, 12, 36, 4, 1, 1, 1, 1, 1, 1, 1, 1, 21, 1, 1] 78
rigid atoms, others: [32, 33, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 34, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25])
total number of confs: 104
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043556 none O=C(CO)N[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 26, 21, 21, 21, 21, 21, 21, 21, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 26, 26, 78, 23, 21, 21, 21, 21, 21, 21, 21, 21, 1, 21, 21] 78
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 140
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043556 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043556
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043556/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043556
Building REAL250005043557
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043557'
/scratch/stefan/7916125/working/building/REAL250005043557 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043557

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043557/0 /scratch/stefan/7916125/working/building/REAL250005043557 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/665
`/scratch/stefan/7916125/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043557 none CCC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 1, 1] 13
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 38, 37, 21, 27, 28, 29, 30, 31] set([0, 1, 3, 36, 35, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26])
total number of confs: 30
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043557 none CCC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 6, 6] 13
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 39
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043557 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043557
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043557/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043557
Building REAL250005043558
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043558'
/scratch/stefan/7916125/working/building/REAL250005043558 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043558

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043558/0 /scratch/stefan/7916125/working/building/REAL250005043558 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/666
`/scratch/stefan/7916125/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043558 none CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 1, 1] 7
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 2, 33, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043558 none CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
7  conformations in input
total number of sets (complete confs): 7
using default count positions algorithm for smaller data
unique positions, atoms: [7, 5, 7, 5, 5, 5, 5, 5, 5, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 5, 5] 7
rigid atoms, others: [33, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35])
total number of confs: 19
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043558 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043558
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043558/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043558
Building REAL250005043559
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043559'
/scratch/stefan/7916125/working/building/REAL250005043559 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043559

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043559/0 /scratch/stefan/7916125/working/building/REAL250005043559 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/667
`/scratch/stefan/7916125/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043559 none O=C(CO)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [4, 1, 4, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 1, 13, 13, 39, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 1, 1] 48
rigid atoms, others: [32, 1, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 34, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24])
total number of confs: 96
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043559 none O=C(CO)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [11, 7, 11, 16, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 16, 16, 48, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 7, 7] 48
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 105
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043559 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043559
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043559/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043559
Building REAL250005043560
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043560'
/scratch/stefan/7916125/working/building/REAL250005043560 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043560

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043560/0 /scratch/stefan/7916125/working/building/REAL250005043560 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/668
`/scratch/stefan/7916125/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043560 none C=CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 1, 1] 13
rigid atoms, others: [32, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 33, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24])
total number of confs: 37
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043560 none C=CC(=O)N1C[C@@H]2CCC[C@]2(NC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
13  conformations in input
total number of sets (complete confs): 13
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 9, 13, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 9, 9] 13
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 31
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043560 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043560
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043560/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043560
Building REAL250005043561
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043561'
/scratch/stefan/7916125/working/building/REAL250005043561 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043561

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043561/0 /scratch/stefan/7916125/working/building/REAL250005043561 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/669
`/scratch/stefan/7916125/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1C[C@@H]2CCC[C@]2(CNC(=O)C2=CC(=O)[N-]O2)C1)

`REAL250005043561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043561 none CC(=O)N1C[C@@H]2CCC[C@]2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 27, 27, 27, 27, 27, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 21, 27, 1, 1] 39
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 38, 37, 21, 25, 26, 27, 28, 29, 30, 31] set([0, 33, 2, 34, 36, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24])
total number of confs: 89
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043561 none CC(=O)N1C[C@@H]2CCC[C@]2(CNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', '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, 7, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [39, 27, 39, 27, 27, 27, 27, 27, 27, 27, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 27, 39, 39, 39, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 6, 1, 27, 27] 39
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 113
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043561 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043561
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043561/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043561
Building REAL250005043562
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043562'
/scratch/stefan/7916125/working/building/REAL250005043562 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043562

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043562/0 /scratch/stefan/7916125/working/building/REAL250005043562 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/670
`/scratch/stefan/7916125/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2)

`REAL250005043562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043562 none CC(=O)NC[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [33, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 1, 33, 33, 33, 33, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 31, 1, 1] 92
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 37, 21, 38, 28, 29, 30, 31] set([0, 1, 2, 3, 36, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27])
total number of confs: 134
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043562 none CC(=O)NC[C@]12CCC[C@H]1CN(C(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 80, 31, 31, 31, 31, 31, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 92, 92, 92, 92, 80, 80, 31, 31, 31, 31, 31, 31, 31, 31, 1, 31, 31] 92
rigid atoms, others: [36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 306
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043562 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043562
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043562/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043562
Building REAL250005043563
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043563'
/scratch/stefan/7916125/working/building/REAL250005043563 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043563

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043563/0 /scratch/stefan/7916125/working/building/REAL250005043563 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/671
`/scratch/stefan/7916125/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043563 none CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 17, 17, 17, 16, 16, 1, 1, 1, 1, 27, 1, 1, 1, 1] 61
rigid atoms, others: [2, 4, 5, 6, 7, 8, 16, 17, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 27])
total number of confs: 107
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043563 none CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 27, 61, 27, 27, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 61, 61, 61, 61, 61, 27, 27, 27, 27, 1, 27, 27, 27, 27] 61
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 158
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043563 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043563
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043563/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043563
Building REAL250005043564
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043564'
/scratch/stefan/7916125/working/building/REAL250005043564 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043564

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043564/0 /scratch/stefan/7916125/working/building/REAL250005043564 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/672
`/scratch/stefan/7916125/working/3D/672' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043564 none COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [63, 33, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 63, 63, 63, 33, 33, 19, 19, 1, 1, 1, 1, 29, 1, 1, 1, 1] 143
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 234
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043564 none COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 141, 111, 84, 29, 84, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 29, 143, 143, 143, 141, 141, 111, 111, 29, 29, 29, 29, 1, 29, 29, 29, 29] 143
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 534
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043564 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043564
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043564/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043564
Building REAL250005043565
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043565'
/scratch/stefan/7916125/working/building/REAL250005043565 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043565

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043565/0 /scratch/stefan/7916125/working/building/REAL250005043565 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/673
`/scratch/stefan/7916125/working/3D/673' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1)

`REAL250005043565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043565 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 44, 44, 65, 65, 26, 26, 1, 26, 26, 26, 26, 65, 65, 65, 65, 65, 26, 26, 26, 26] 65
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043565 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 6, 6, 17, 17, 1, 1, 26, 1, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 1, 1] 65
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 17, 18, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 19, 24, 25, 26, 27, 28])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043565 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [53, 17, 53, 65, 65, 65, 65, 65, 17, 17, 17, 8, 1, 8, 1, 1, 1, 17, 17, 65, 17, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17] 65
rigid atoms, others: [12, 14, 15, 16, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32])
total number of confs: 157
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043565 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043565
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043565/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043565
Building REAL250005043566
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043566'
/scratch/stefan/7916125/working/building/REAL250005043566 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043566

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043566/0 /scratch/stefan/7916125/working/building/REAL250005043566 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/674
`/scratch/stefan/7916125/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1)

`REAL250005043566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043566 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 71, 71, 93, 93, 93, 29, 29, 1, 29, 29, 29, 29, 93, 93, 93, 93, 93, 93, 93, 29, 29, 29, 29] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 259
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043566 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 1, 1, 29, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 93
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 97
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: REAL250005043566 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [73, 21, 73, 93, 93, 93, 93, 93, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 21, 21, 93, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 93
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35])
total number of confs: 215
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043566 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043566
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043566/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043566
Building REAL250005043567
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043567'
/scratch/stefan/7916125/working/building/REAL250005043567 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043567

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043567/0 /scratch/stefan/7916125/working/building/REAL250005043567 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/675
`/scratch/stefan/7916125/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1)

`REAL250005043567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043567 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 79, 79, 101, 101, 101, 101, 30, 30, 1, 30, 30, 30, 30, 101, 101, 101, 101, 101, 101, 101, 101, 101, 30, 30, 30, 30] 101
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 286
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043567 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 1, 1, 30, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 101
rigid atoms, others: [1, 35, 36, 37, 38, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 98
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: REAL250005043567 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [73, 21, 73, 101, 101, 101, 101, 101, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 21, 21, 101, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 101
rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38])
total number of confs: 220
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043567 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043567
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043567/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043567
Building REAL250005043568
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043568'
/scratch/stefan/7916125/working/building/REAL250005043568 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043568

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043568/0 /scratch/stefan/7916125/working/building/REAL250005043568 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/676
`/scratch/stefan/7916125/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043568 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [19, 3, 1, 1, 1, 1, 19, 41, 41, 41, 41, 137, 137, 171, 171, 171, 171, 171, 41, 41, 3, 3, 1, 1, 1, 1, 1, 41, 41, 41, 41, 171, 41, 41, 41, 41] 171
rigid atoms, others: [2, 3, 4, 5, 22, 23, 24, 25, 26] set([0, 1, 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])
total number of confs: 404
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043568 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 26, 41, 41, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 26, 26, 41, 41, 41, 41, 41, 1, 1, 1, 1, 35, 1, 1, 1, 1] 171
rigid atoms, others: [32, 1, 34, 35, 33, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 197
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: REAL250005043568 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [97, 35, 97, 141, 171, 171, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 141, 141, 171, 171, 171, 171, 171, 35, 35, 35, 35, 1, 35, 35, 35, 35] 171
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 581
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043568 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043568
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043568/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043568
Building REAL250005043569
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043569'
/scratch/stefan/7916125/working/building/REAL250005043569 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043569

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043569/0 /scratch/stefan/7916125/working/building/REAL250005043569 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/677
`/scratch/stefan/7916125/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043569 none CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 11, 11, 1, 5, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 23, 1, 1, 1, 1] 81
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 77
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043569 none CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 54, 81, 81, 23, 54, 23, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 23, 81, 81, 81, 81, 81, 81, 23, 23, 23, 23, 1, 23, 23, 23, 23] 81
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 296
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043569 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043569
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043569/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043569
Building REAL250005043570
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043570'
/scratch/stefan/7916125/working/building/REAL250005043570 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043570

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043570/0 /scratch/stefan/7916125/working/building/REAL250005043570 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/678
`/scratch/stefan/7916125/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043570 none CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [17, 7, 17, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 17, 17, 17, 1, 1, 1, 1, 29, 1, 1, 1, 1] 68
rigid atoms, others: [4, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 27])
total number of confs: 99
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043570 none CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 59, 68, 68, 29, 59, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 68, 68, 68, 29, 29, 29, 29, 1, 29, 29, 29, 29] 68
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 183
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043570 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043570
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043570/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043570
Building REAL250005043571
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043571'
/scratch/stefan/7916125/working/building/REAL250005043571 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043571

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043571/0 /scratch/stefan/7916125/working/building/REAL250005043571 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/679
`/scratch/stefan/7916125/working/3D/679' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043571 none COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [64, 28, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 65, 65, 65, 28, 28, 1, 1, 1, 1, 37, 1, 1, 1, 1] 175
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 207
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043571 none COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 165, 101, 37, 101, 37, 37, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 175, 175, 175, 165, 165, 37, 37, 37, 37, 1, 37, 37, 37, 37] 175
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 588
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043571 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043571
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043571/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043571
Building REAL250005043572
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043572'
/scratch/stefan/7916125/working/building/REAL250005043572 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043572

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043572/0 /scratch/stefan/7916125/working/building/REAL250005043572 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/680
`/scratch/stefan/7916125/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043572 none CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [41, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 44, 44, 44, 43, 43, 27, 27, 1, 1, 1, 1, 29, 1, 1, 1, 1] 149
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 248
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043572 none CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [149, 145, 88, 29, 88, 29, 29, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 149, 149, 149, 149, 149, 145, 145, 29, 29, 29, 29, 1, 29, 29, 29, 29] 149
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 550
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043572 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043572
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043572/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043572
Building REAL250005043573
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043573'
/scratch/stefan/7916125/working/building/REAL250005043573 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043573

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043573/0 /scratch/stefan/7916125/working/building/REAL250005043573 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/681
`/scratch/stefan/7916125/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043573 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 98, 98, 116, 116, 116, 116, 116, 33, 33, 1, 1, 1, 33, 33, 33, 33, 116, 33, 33, 33, 33] 116
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043573 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 33, 33, 33, 1, 1, 1, 1, 33, 1, 1, 1, 1] 116
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043573 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [86, 33, 86, 116, 116, 116, 116, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 116, 116, 116, 33, 33, 33, 33, 1, 33, 33, 33, 33] 116
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 269
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043573 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043573
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043573/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043573
Building REAL250005043574
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043574'
/scratch/stefan/7916125/working/building/REAL250005043574 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043574

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043574/0 /scratch/stefan/7916125/working/building/REAL250005043574 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/682
`/scratch/stefan/7916125/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043574 none CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [59, 58, 59, 25, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 59, 59, 59, 58, 25, 25, 1, 1, 1, 1, 29, 1, 1, 1, 1] 138
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 224
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043574 none CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 115, 88, 29, 88, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 138, 138, 138, 138, 115, 115, 29, 29, 29, 29, 1, 29, 29, 29, 29] 138
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 435
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043574 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043574
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043574/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043574
Building REAL250005043575
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043575'
/scratch/stefan/7916125/working/building/REAL250005043575 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043575

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043575/0 /scratch/stefan/7916125/working/building/REAL250005043575 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/683
`/scratch/stefan/7916125/working/3D/683' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043575 none CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [28, 23, 32, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 32, 32, 32, 32, 32, 32, 32, 23, 23, 1, 1, 1, 1, 32, 1, 1, 1, 1] 120
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 205
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043575 none CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [117, 116, 120, 83, 32, 83, 32, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 32, 120, 120, 120, 120, 120, 120, 120, 116, 116, 32, 32, 32, 32, 1, 32, 32, 32, 32] 120
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 401
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043575 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043575
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043575/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043575
Building REAL250005043576
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043576'
/scratch/stefan/7916125/working/building/REAL250005043576 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043576

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043576/0 /scratch/stefan/7916125/working/building/REAL250005043576 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/684
`/scratch/stefan/7916125/working/3D/684' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043576 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 60, 60, 72, 72, 72, 72, 72, 21, 21, 2, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 72, 21, 21, 21, 21] 72
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([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])
total number of confs: 170
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043576 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 28, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 96
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: REAL250005043576 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 28, 62, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 72, 72, 72, 72, 72, 72, 72, 28, 28, 28, 28, 1, 28, 28, 28, 28] 72
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 185
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043576 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043576
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043576/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043576
Building REAL250005043577
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043577'
/scratch/stefan/7916125/working/building/REAL250005043577 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043577

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043577/0 /scratch/stefan/7916125/working/building/REAL250005043577 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/685
`/scratch/stefan/7916125/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043577 none CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 77, 77, 77, 76, 76, 24, 24, 1, 1, 1, 1, 23, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 236
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043577 none CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 85, 23, 85, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 159, 159, 23, 23, 23, 23, 1, 23, 23, 23, 23] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 652
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043577 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043577
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043577/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043577
Building REAL250005043578
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043578'
/scratch/stefan/7916125/working/building/REAL250005043578 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043578

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043578/0 /scratch/stefan/7916125/working/building/REAL250005043578 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/686
`/scratch/stefan/7916125/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043578 none CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 31, 1, 1, 1, 1] 95
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043578 none CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 73, 31, 71, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 95, 95, 95, 95, 95, 95, 95, 31, 31, 31, 31, 1, 31, 31, 31, 31] 95
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 275
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043578 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043578
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043578/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043578
Building REAL250005043579
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043579'
/scratch/stefan/7916125/working/building/REAL250005043579 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043579

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043579/0 /scratch/stefan/7916125/working/building/REAL250005043579 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/687
`/scratch/stefan/7916125/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1)

`REAL250005043579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043579 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 80, 80, 98, 98, 98, 98, 28, 28, 1, 28, 28, 28, 28, 98, 98, 98, 98, 98, 98, 98, 28, 28, 28, 28] 98
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 258
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043579 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 1, 28, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 98
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 98
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: REAL250005043579 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [82, 23, 82, 98, 98, 98, 98, 98, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 23, 23, 98, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 98
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 224
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043579 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043579
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043579/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043579
Building REAL250005043580
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043580'
/scratch/stefan/7916125/working/building/REAL250005043580 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043580

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043580/0 /scratch/stefan/7916125/working/building/REAL250005043580 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/688
`/scratch/stefan/7916125/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043580 none CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 26, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 87, 87, 87, 26, 26, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 211
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043580 none CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 73, 19, 73, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 149, 149, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 651
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043580 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043580
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043580/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043580
Building REAL250005043581
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043581'
/scratch/stefan/7916125/working/building/REAL250005043581 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043581

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043581/0 /scratch/stefan/7916125/working/building/REAL250005043581 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/689
`/scratch/stefan/7916125/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043581 none CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 63, 63, 63, 20, 20, 18, 18, 1, 1, 1, 1, 33, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 183
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043581 none CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 117, 93, 33, 93, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 33, 201, 201, 201, 119, 119, 117, 117, 33, 33, 33, 33, 1, 33, 33, 33, 33] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 500
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043581 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043581
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043581/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043581
Building REAL250005043582
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043582'
/scratch/stefan/7916125/working/building/REAL250005043582 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043582

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043582/0 /scratch/stefan/7916125/working/building/REAL250005043582 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/690
`/scratch/stefan/7916125/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043582 none CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 27, 34, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 34, 34, 34, 34, 34, 34, 34, 27, 27, 19, 19, 1, 1, 1, 1, 28, 1, 1, 1, 1] 133
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 195
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043582 none CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 129, 133, 116, 81, 28, 81, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 133, 133, 133, 133, 133, 133, 133, 129, 129, 116, 116, 28, 28, 28, 28, 1, 28, 28, 28, 28] 133
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043582 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043582
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043582/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043582
Building REAL250005043583
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043583'
/scratch/stefan/7916125/working/building/REAL250005043583 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043583

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043583/0 /scratch/stefan/7916125/working/building/REAL250005043583 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/691
`/scratch/stefan/7916125/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043583 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 77, 77, 107, 107, 107, 107, 107, 27, 27, 1, 1, 1, 1, 27, 27, 27, 27, 107, 27, 27, 27, 27] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 238
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043583 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 27, 27, 27, 27, 1, 1, 1, 1, 29, 1, 1, 1, 1] 107
rigid atoms, others: [32, 1, 33, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 83
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043583 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 29, 66, 107, 107, 107, 107, 29, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 107, 107, 107, 107, 29, 29, 29, 29, 1, 29, 29, 29, 29] 107
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 241
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043583 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043583
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043583/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043583
Building REAL250005043584
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043584'
/scratch/stefan/7916125/working/building/REAL250005043584 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043584

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043584/0 /scratch/stefan/7916125/working/building/REAL250005043584 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/692
`/scratch/stefan/7916125/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043584 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 79, 79, 106, 106, 106, 106, 106, 27, 27, 1, 1, 1, 27, 27, 27, 27, 106, 27, 27, 27, 27] 106
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043584 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 27, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1] 106
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043584 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [73, 33, 73, 106, 106, 106, 106, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 106, 106, 106, 33, 33, 33, 33, 1, 33, 33, 33, 33] 106
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 241
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043584 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043584
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043584/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043584
Building REAL250005043585
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043585'
/scratch/stefan/7916125/working/building/REAL250005043585 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043585

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043585/0 /scratch/stefan/7916125/working/building/REAL250005043585 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/693
`/scratch/stefan/7916125/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043585 none CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 42, 28, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 50, 50, 50, 50, 50, 42, 42, 30, 30, 18, 18, 1, 1, 1, 1, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 293
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043585 none CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 140, 83, 21, 83, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 201, 201, 162, 162, 140, 140, 21, 21, 21, 21, 1, 21, 21, 21, 21] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 829
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043585 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043585
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043585/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043585
Building REAL250005043586
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043586'
/scratch/stefan/7916125/working/building/REAL250005043586 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043586

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043586/0 /scratch/stefan/7916125/working/building/REAL250005043586 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/694
`/scratch/stefan/7916125/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043586 none CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [24, 17, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 1, 1, 1, 1, 28, 1, 1, 1, 1] 121
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 143
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043586 none CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 117, 121, 121, 82, 28, 82, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 121, 121, 121, 121, 121, 121, 121, 121, 121, 117, 117, 28, 28, 28, 28, 1, 28, 28, 28, 28] 121
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 414
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043586 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043586
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043586/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043586
Building REAL250005043587
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043587'
/scratch/stefan/7916125/working/building/REAL250005043587 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043587

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043587/0 /scratch/stefan/7916125/working/building/REAL250005043587 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/695
`/scratch/stefan/7916125/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043587 none CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [46, 31, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 47, 47, 47, 46, 46, 35, 35, 19, 19, 1, 1, 1, 1, 28, 1, 1, 1, 1] 168
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 283
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043587 none CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 158, 135, 88, 28, 88, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 168, 168, 168, 168, 168, 158, 158, 135, 135, 28, 28, 28, 28, 1, 28, 28, 28, 28] 168
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 652
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043587 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043587
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043587/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043587
Building REAL250005043588
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043588'
/scratch/stefan/7916125/working/building/REAL250005043588 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043588

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043588/0 /scratch/stefan/7916125/working/building/REAL250005043588 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/696
`/scratch/stefan/7916125/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043588 none CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 30, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 106
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043588 none CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 30, 71, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 71, 71, 71, 71, 71, 71, 71, 30, 30, 30, 30, 1, 30, 30, 30, 30] 71
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 174
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043588 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043588
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043588/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043588
Building REAL250005043589
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043589'
/scratch/stefan/7916125/working/building/REAL250005043589 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043589

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043589/0 /scratch/stefan/7916125/working/building/REAL250005043589 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/697
`/scratch/stefan/7916125/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043589 none CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 32, 32, 32, 32, 32, 18, 18, 18, 18, 1, 1, 1, 1, 35, 1, 1, 1, 1] 128
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 213
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043589 none CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 95, 121, 35, 95, 35, 35, 35, 11, 1, 11, 1, 1, 1, 1, 1, 1, 35, 35, 128, 128, 128, 128, 128, 121, 121, 121, 121, 35, 35, 35, 35, 1, 35, 35, 35, 35] 128
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 418
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043589 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043589
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043589/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043589
Building REAL250005043590
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043590'
/scratch/stefan/7916125/working/building/REAL250005043590 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043590

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043590/0 /scratch/stefan/7916125/working/building/REAL250005043590 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/698
`/scratch/stefan/7916125/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043590 none CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [20, 13, 7, 13, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 22, 22, 22, 22, 22, 13, 22, 22, 22, 22, 22, 1, 1, 1, 1, 30, 1, 1, 1, 1] 173
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 214
number of broken/clashed sets: 104
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043590 none CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [155, 137, 118, 137, 157, 30, 118, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 157, 157, 157, 157, 157, 137, 159, 159, 159, 159, 159, 30, 30, 30, 30, 1, 30, 30, 30, 30] 173
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 665
number of broken/clashed sets: 104
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043590 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043590
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043590/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043590
Building REAL250005043591
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043591'
/scratch/stefan/7916125/working/building/REAL250005043591 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043591

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043591/0 /scratch/stefan/7916125/working/building/REAL250005043591 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/699
`/scratch/stefan/7916125/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 104, 104, 124, 124, 124, 124, 124, 36, 36, 1, 1, 1, 36, 36, 36, 36, 124, 36, 36, 36, 36] 124
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 36, 36, 36, 36, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 36, 36, 36, 1, 1, 1, 1, 33, 1, 1, 1, 1] 124
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [93, 33, 91, 124, 124, 124, 124, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 124, 124, 124, 33, 33, 33, 33, 1, 33, 33, 33, 33] 124
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 288
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043591 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043591/1 /scratch/stefan/7916125/working/building/REAL250005043591 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/700
`/scratch/stefan/7916125/working/3D/700' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043591.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043591/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 76, 76, 99, 99, 99, 99, 99, 25, 25, 1, 1, 1, 25, 25, 25, 25, 99, 25, 25, 25, 25] 99
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 25, 25, 25, 25, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 25, 25, 25, 1, 1, 1, 1, 30, 1, 1, 1, 1] 99
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043591 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [69, 30, 69, 99, 99, 99, 99, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 99, 99, 99, 30, 30, 30, 30, 1, 30, 30, 30, 30] 99
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 226
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043591 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043591
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043591/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043591/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043591
Building REAL250005043592
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043592'
/scratch/stefan/7916125/working/building/REAL250005043592 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043592

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043592/0 /scratch/stefan/7916125/working/building/REAL250005043592 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/701
`/scratch/stefan/7916125/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043592 none CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [58, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 56, 58, 58, 15, 15, 15, 15, 1, 1, 1, 1, 38, 1, 1, 1, 1] 174
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 167
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043592 none CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 128, 109, 128, 32, 109, 38, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 174, 174, 174, 128, 128, 128, 128, 38, 38, 38, 38, 1, 38, 38, 38, 38] 174
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 469
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043592 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043592
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043592/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043592
Building REAL250005043593
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043593'
/scratch/stefan/7916125/working/building/REAL250005043593 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043593

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043593/0 /scratch/stefan/7916125/working/building/REAL250005043593 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/702
`/scratch/stefan/7916125/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043593 none CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 36, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 37, 37, 37, 37, 37, 18, 18, 18, 18, 1, 1, 1, 1, 36, 1, 1, 1, 1] 142
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 149
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043593 none CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 119, 92, 119, 36, 93, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 142, 142, 142, 142, 142, 119, 119, 119, 119, 36, 36, 36, 36, 1, 36, 36, 36, 36] 142
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 423
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043593 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043593
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043593/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043593
Building REAL250005043594
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043594'
/scratch/stefan/7916125/working/building/REAL250005043594 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043594

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043594/0 /scratch/stefan/7916125/working/building/REAL250005043594 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/703
`/scratch/stefan/7916125/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043594 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 39, 39, 55, 55, 55, 55, 55, 15, 15, 1, 1, 1, 15, 15, 15, 15, 55, 15, 15, 15, 15] 55
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043594 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 14, 14, 14, 1, 1, 1, 1, 28, 1, 1, 1, 1] 54
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 68
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043594 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 28, 54, 54, 54, 54, 54, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 54, 54, 54, 28, 28, 28, 28, 1, 28, 28, 28, 28] 54
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 128
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043594 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043594
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043594/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043594
Building REAL250005043595
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043595'
/scratch/stefan/7916125/working/building/REAL250005043595 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043595

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043595/0 /scratch/stefan/7916125/working/building/REAL250005043595 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/704
`/scratch/stefan/7916125/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043595 none COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 30, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 111, 111, 111, 63, 63, 32, 32, 18, 18, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 419
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043595 none COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 114, 81, 53, 15, 53, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 199, 200, 120, 120, 81, 81, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 922
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043595 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043595
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043595/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043595
Building REAL250005043596
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043596'
/scratch/stefan/7916125/working/building/REAL250005043596 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043596

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043596/0 /scratch/stefan/7916125/working/building/REAL250005043596 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/705
`/scratch/stefan/7916125/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1)

`REAL250005043596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043596 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 93, 93, 131, 131, 131, 131, 33, 33, 1, 33, 33, 33, 33, 131, 131, 33, 33, 33, 33] 131
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043596 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 1, 1, 33, 1, 1, 1, 1, 39, 39, 1, 1, 1, 1] 131
rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043596 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [103, 39, 103, 131, 131, 131, 131, 131, 39, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 39, 39, 131, 39, 39, 39, 39, 1, 1, 39, 39, 39, 39] 131
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 301
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043596 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043596
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043596/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043596
Building REAL250005043597
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043597'
/scratch/stefan/7916125/working/building/REAL250005043597 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043597

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043597/0 /scratch/stefan/7916125/working/building/REAL250005043597 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/706
`/scratch/stefan/7916125/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043597 none CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 30, 30, 7, 30, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 60, 60, 60, 60, 60, 30, 30, 30, 30, 1, 1, 1, 1, 33, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043597 none CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 184, 113, 184, 33, 113, 33, 33, 32, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 184, 184, 184, 184, 33, 33, 33, 33, 1, 33, 33, 33, 33] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 621
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043597 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043597
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043597/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043597
Building REAL250005043598
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043598'
/scratch/stefan/7916125/working/building/REAL250005043598 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043598

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043598/0 /scratch/stefan/7916125/working/building/REAL250005043598 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/707
`/scratch/stefan/7916125/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043598 none COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [34, 21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 34, 34, 34, 21, 21, 21, 21, 1, 1, 1, 1, 35, 1, 1, 1, 1] 115
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 146
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043598 none COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 112, 95, 112, 35, 95, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 115, 115, 115, 112, 112, 112, 112, 35, 35, 35, 35, 1, 35, 35, 35, 35] 115
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 336
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043598 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043598
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043598/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043598
Building REAL250005043599
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043599'
/scratch/stefan/7916125/working/building/REAL250005043599 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043599

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043599/0 /scratch/stefan/7916125/working/building/REAL250005043599 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/708
`/scratch/stefan/7916125/working/3D/708' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043599 none CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 90, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 90, 90, 90, 90, 90, 90, 90, 22, 22, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043599 none CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 99, 50, 15, 50, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201, 201, 201, 201, 99, 99, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 645
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043599 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043599
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043599/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043599
Building REAL250005043600
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043600'
/scratch/stefan/7916125/working/building/REAL250005043600 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043600

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043600/0 /scratch/stefan/7916125/working/building/REAL250005043600 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/709
`/scratch/stefan/7916125/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043600 none CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 66, 40, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 91, 91, 91, 91, 91, 66, 66, 18, 18, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 383
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043600 none CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 134, 82, 39, 13, 39, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 173, 173, 82, 82, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 768
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043600 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043600
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043600/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043600
Building REAL250005043601
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043601'
/scratch/stefan/7916125/working/building/REAL250005043601 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043601

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043601/0 /scratch/stefan/7916125/working/building/REAL250005043601 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/710
`/scratch/stefan/7916125/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1)

`REAL250005043601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043601 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 75, 75, 99, 99, 99, 99, 30, 30, 1, 30, 30, 30, 30, 98, 99, 99, 99, 99, 99, 99, 30, 30, 30, 30] 99
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 285
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043601 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 1, 1, 30, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1] 99
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 100
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: REAL250005043601 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [73, 22, 75, 99, 99, 99, 99, 99, 22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 22, 22, 99, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22] 99
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 222
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043601 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043601
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043601/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043601
Building REAL250005043602
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043602'
/scratch/stefan/7916125/working/building/REAL250005043602 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043602

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043602/0 /scratch/stefan/7916125/working/building/REAL250005043602 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/711
`/scratch/stefan/7916125/working/3D/711' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043602 none CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 24, 7, 24, 35, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 41, 41, 41, 41, 41, 24, 35, 35, 35, 1, 1, 1, 1, 30, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 264
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043602 none CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 188, 106, 188, 198, 30, 106, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 198, 198, 198, 198, 198, 188, 198, 198, 198, 30, 30, 30, 30, 1, 30, 30, 30, 30] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 779
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043602 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043602
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043602/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043602
Building REAL250005043603
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043603'
/scratch/stefan/7916125/working/building/REAL250005043603 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043603

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043603/0 /scratch/stefan/7916125/working/building/REAL250005043603 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/712
`/scratch/stefan/7916125/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043603 none COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 60, 31, 60, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 79, 79, 79, 60, 60, 60, 60, 31, 31, 1, 1, 1, 1, 26, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 328
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043603 none COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 166, 200, 88, 26, 88, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 201, 200, 200, 200, 200, 166, 166, 26, 26, 26, 26, 1, 26, 26, 26, 26] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 779
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043603 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043603
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043603/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043603
Building REAL250005043604
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043604'
/scratch/stefan/7916125/working/building/REAL250005043604 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043604

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043604/0 /scratch/stefan/7916125/working/building/REAL250005043604 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/713
`/scratch/stefan/7916125/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043604 none C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 69, 69, 69, 26, 26, 16, 16, 1, 1, 1, 1, 33, 1, 1, 1, 1] 164
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 283
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043604 none C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 145, 103, 33, 103, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 164, 164, 164, 164, 164, 145, 145, 33, 33, 33, 33, 1, 33, 33, 33, 33] 164
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 585
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043604 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043604
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043604/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043604
Building REAL250005043605
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043605'
/scratch/stefan/7916125/working/building/REAL250005043605 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043605

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043605/0 /scratch/stefan/7916125/working/building/REAL250005043605 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/714
`/scratch/stefan/7916125/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043605 none CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 37, 21, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 99, 99, 99, 98, 98, 37, 37, 21, 21, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 356
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043605 none CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 148, 114, 75, 19, 75, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 201, 148, 148, 114, 114, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 644
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043605 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043605
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043605/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043605
Building REAL250005043606
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043606'
/scratch/stefan/7916125/working/building/REAL250005043606 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043606

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043606/0 /scratch/stefan/7916125/working/building/REAL250005043606 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/715
`/scratch/stefan/7916125/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043606 none COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 102, 102, 102, 61, 61, 19, 19, 19, 19, 1, 1, 1, 1, 23, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 346
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043606 none COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 138, 89, 138, 23, 89, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 138, 138, 138, 138, 23, 23, 23, 23, 1, 23, 23, 23, 23] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 830
number of broken/clashed sets: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043606 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043606
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043606/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043606
Building REAL250005043607
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043607'
/scratch/stefan/7916125/working/building/REAL250005043607 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043607

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043607/0 /scratch/stefan/7916125/working/building/REAL250005043607 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/716
`/scratch/stefan/7916125/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043607 none C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 37, 15, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 99, 99, 99, 83, 83, 15, 15, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043607 none C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 79, 49, 13, 49, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 79, 79, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043607 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043607
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043607/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043607
Building REAL250005043608
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043608'
/scratch/stefan/7916125/working/building/REAL250005043608 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043608

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043608/0 /scratch/stefan/7916125/working/building/REAL250005043608 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/717
`/scratch/stefan/7916125/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043608 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 93, 93, 111, 111, 111, 111, 111, 34, 34, 1, 1, 34, 34, 34, 34, 111, 34, 34, 34, 34] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043608 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 34, 34, 34, 34, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 34, 34, 1, 1, 1, 1, 33, 1, 1, 1, 1] 111
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043608 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [85, 33, 85, 111, 111, 111, 111, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 111, 111, 33, 33, 33, 33, 1, 33, 33, 33, 33] 111
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 251
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043608 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043608
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043608/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043608
Building REAL250005043609
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043609'
/scratch/stefan/7916125/working/building/REAL250005043609 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043609

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043609/0 /scratch/stefan/7916125/working/building/REAL250005043609 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/718
`/scratch/stefan/7916125/working/3D/718' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043609 none CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 59, 59, 59, 59, 56, 52, 52, 19, 19, 19, 19, 1, 1, 1, 1, 31, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 304
number of broken/clashed sets: 102
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043609 none CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 169, 118, 169, 31, 118, 31, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 197, 201, 201, 169, 169, 169, 169, 31, 31, 31, 31, 1, 31, 31, 31, 31] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 769
number of broken/clashed sets: 102
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043609 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043609
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043609/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043609
Building REAL250005043610
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043610'
/scratch/stefan/7916125/working/building/REAL250005043610 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043610

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043610/0 /scratch/stefan/7916125/working/building/REAL250005043610 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/719
`/scratch/stefan/7916125/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043610 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 7, 3, 1, 1, 1, 1, 31, 60, 60, 60, 60, 177, 177, 201, 201, 201, 201, 201, 60, 60, 7, 7, 3, 3, 1, 1, 1, 1, 1, 60, 60, 60, 60, 201, 60, 60, 60, 60] 201
rigid atoms, others: [3, 4, 5, 6, 25, 26, 27, 28, 29] set([0, 1, 2, 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])
total number of confs: 490
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043610 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 36, 60, 60, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 20, 20, 38, 38, 60, 60, 60, 60, 60, 1, 1, 1, 1, 29, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 35, 36, 33, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 305
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: REAL250005043610 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 84, 135, 151, 201, 201, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 135, 135, 153, 153, 201, 201, 201, 201, 201, 29, 29, 29, 29, 1, 29, 29, 29, 29] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 763
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043610 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043610
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043610/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043610
Building REAL250005043611
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043611'
/scratch/stefan/7916125/working/building/REAL250005043611 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043611

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043611/0 /scratch/stefan/7916125/working/building/REAL250005043611 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/720
`/scratch/stefan/7916125/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1)

`REAL250005043611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043611 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 64, 64, 93, 93, 93, 93, 28, 28, 1, 28, 28, 28, 28, 93, 93, 93, 93, 93, 93, 93, 28, 28, 28, 28] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 271
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043611 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 1, 28, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 93
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 88
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: REAL250005043611 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [69, 17, 69, 93, 93, 93, 93, 93, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 17, 17, 93, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 93
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 207
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043611 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043611
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043611/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043611
Building REAL250005043612
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043612'
/scratch/stefan/7916125/working/building/REAL250005043612 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043612

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043612/0 /scratch/stefan/7916125/working/building/REAL250005043612 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/721
`/scratch/stefan/7916125/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043612 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [26, 6, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 148, 148, 177, 177, 177, 177, 177, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 177, 50, 50, 50, 50] 177
rigid atoms, others: [2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 430
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043612 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 27, 50, 50, 50, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 36, 1, 1, 1, 1] 177
rigid atoms, others: [32, 1, 35, 36, 33, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 211
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: REAL250005043612 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [106, 36, 106, 140, 177, 177, 177, 36, 36, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 140, 140, 177, 177, 177, 177, 177, 177, 177, 36, 36, 36, 36, 1, 36, 36, 36, 36] 177
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 589
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043612 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043612
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043612/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043612
Building REAL250005043613
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043613'
/scratch/stefan/7916125/working/building/REAL250005043613 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043613

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043613/0 /scratch/stefan/7916125/working/building/REAL250005043613 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/722
`/scratch/stefan/7916125/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1)

`REAL250005043613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043613 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 16, 22, 22, 16, 16, 16, 16, 1, 1, 1, 1, 33, 1, 1, 1, 1, 22, 22, 22, 22, 22] 94
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 16, 17, 25, 26, 27, 28, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38])
total number of confs: 130
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043613 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 33, 75, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 94, 94, 94, 94, 94, 94, 94, 33, 33, 33, 33, 1, 33, 33, 33, 33, 94, 94, 94, 94, 94] 94
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 295
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: REAL250005043613 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 11, 11, 22, 22, 22, 22, 69, 69, 94, 94, 94, 94, 94, 22, 22, 1, 1, 1, 4, 4, 4, 3, 22, 22, 22, 22, 94, 22, 22, 22, 22, 1, 1, 1, 1, 1] 94
rigid atoms, others: [1, 34, 35, 36, 37, 38, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 226
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043613 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043613
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043613/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043613
Building REAL250005043614
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043614'
/scratch/stefan/7916125/working/building/REAL250005043614 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043614

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043614/0 /scratch/stefan/7916125/working/building/REAL250005043614 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/723
`/scratch/stefan/7916125/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043614 none CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 7, 28, 1, 7, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 32, 1, 1, 1, 1] 108
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043614 none CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 64, 108, 32, 64, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 108, 108, 108, 108, 108, 108, 108, 32, 32, 32, 32, 1, 32, 32, 32, 32] 108
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043614 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043614
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043614/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043614
Building REAL250005043615
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043615'
/scratch/stefan/7916125/working/building/REAL250005043615 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043615

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043615/0 /scratch/stefan/7916125/working/building/REAL250005043615 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/724
`/scratch/stefan/7916125/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1)

`REAL250005043615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043615 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 85, 85, 105, 105, 105, 105, 105, 23, 23, 1, 2, 2, 2, 1, 1, 1, 1, 23, 23, 23, 23, 105, 23, 23, 23, 23, 1, 1] 105
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 239
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043615 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 33, 1, 1, 1, 1, 23, 23] 105
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 32, 37, 38])
total number of confs: 105
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: REAL250005043615 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 89, 33, 89, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 105, 105, 105, 105, 105, 105, 105, 105, 33, 33, 33, 33, 1, 33, 33, 33, 33, 105, 105] 105
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043615 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043615
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043615/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043615
Building REAL250005043616
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043616'
/scratch/stefan/7916125/working/building/REAL250005043616 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043616

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043616/0 /scratch/stefan/7916125/working/building/REAL250005043616 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/725
`/scratch/stefan/7916125/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043616 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 149, 149, 187, 187, 187, 187, 187, 44, 43, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 187, 44, 44, 44, 44] 187
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 429
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043616 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 44, 44, 44, 44, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 40, 1, 1, 1, 1] 187
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 154
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: REAL250005043616 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [118, 40, 118, 187, 187, 187, 187, 40, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 187, 187, 187, 187, 187, 187, 187, 40, 40, 40, 40, 1, 40, 40, 40, 40] 187
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 520
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043616 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043616
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043616/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043616
Building REAL250005043617
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043617'
/scratch/stefan/7916125/working/building/REAL250005043617 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043617

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043617/0 /scratch/stefan/7916125/working/building/REAL250005043617 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/726
`/scratch/stefan/7916125/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043617 none CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 7, 25, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 37, 1, 1, 1, 1] 103
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043617 none CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 77, 103, 31, 75, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 103, 103, 103, 103, 103, 103, 37, 37, 37, 37, 1, 37, 37, 37, 37] 103
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043617 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043617
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043617/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043617
Building REAL250005043618
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043618'
/scratch/stefan/7916125/working/building/REAL250005043618 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043618

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043618/0 /scratch/stefan/7916125/working/building/REAL250005043618 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/727
`/scratch/stefan/7916125/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043618 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 62, 62, 78, 78, 78, 78, 78, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 78, 24, 24, 24, 24] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 174
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043618 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 37, 1, 1, 1, 1] 78
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 88
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: REAL250005043618 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 37, 78, 78, 78, 78, 78, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 78, 78, 78, 78, 78, 78, 78, 37, 37, 37, 37, 1, 37, 37, 37, 37] 78
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 189
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043618 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043618
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043618/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043618
Building REAL250005043619
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043619'
/scratch/stefan/7916125/working/building/REAL250005043619 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043619

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043619/0 /scratch/stefan/7916125/working/building/REAL250005043619 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/728
`/scratch/stefan/7916125/working/3D/728' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043619 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 57, 57, 71, 71, 71, 71, 71, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 71, 17, 17, 17, 17] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 168
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043619 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 29, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 89
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: REAL250005043619 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 69, 29, 69, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 71, 29, 29, 29, 29, 1, 29, 29, 29, 29] 71
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 169
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043619 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043619
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043619/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043619
Building REAL250005043620
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043620'
/scratch/stefan/7916125/working/building/REAL250005043620 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043620

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043620/0 /scratch/stefan/7916125/working/building/REAL250005043620 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/729
`/scratch/stefan/7916125/working/3D/729' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043620 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 61, 61, 75, 75, 75, 75, 75, 20, 20, 2, 2, 2, 2, 2, 2, 1, 1, 20, 20, 20, 20, 75, 20, 20, 20, 20] 75
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])
total number of confs: 183
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043620 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 26, 1, 1, 1, 1] 75
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 92
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: REAL250005043620 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 68, 75, 26, 68, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 75, 75, 75, 75, 75, 75, 75, 75, 26, 26, 26, 26, 1, 26, 26, 26, 26] 75
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 193
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043620 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043620
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043620/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043620
Building REAL250005043621
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043621'
/scratch/stefan/7916125/working/building/REAL250005043621 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043621

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043621/0 /scratch/stefan/7916125/working/building/REAL250005043621 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/730
`/scratch/stefan/7916125/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1)

`REAL250005043621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043621 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 79, 79, 97, 97, 97, 97, 97, 28, 28, 1, 28, 28, 28, 28, 97, 97, 97, 97, 97, 97, 28, 28, 28, 28] 97
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 256
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043621 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 28, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 97
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29, 30, 31])
total number of confs: 98
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: REAL250005043621 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [81, 23, 81, 97, 97, 97, 97, 97, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 97, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 97
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 222
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043621 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043621
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043621/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043621
Building REAL250005043622
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043622'
/scratch/stefan/7916125/working/building/REAL250005043622 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043622

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043622/0 /scratch/stefan/7916125/working/building/REAL250005043622 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/731
`/scratch/stefan/7916125/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043622 none CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 25, 46, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 61, 61, 61, 61, 61, 46, 46, 46, 46, 25, 25, 1, 1, 1, 1, 20, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 307
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043622 none CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 153, 190, 84, 20, 84, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 190, 190, 190, 190, 153, 153, 20, 20, 20, 20, 1, 20, 20, 20, 20] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 832
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043622 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043622
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043622/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043622
Building REAL250005043623
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043623'
/scratch/stefan/7916125/working/building/REAL250005043623 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043623

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043623/0 /scratch/stefan/7916125/working/building/REAL250005043623 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/732
`/scratch/stefan/7916125/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043623 none C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 56, 55, 55, 28, 28, 16, 16, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 303
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043623 none C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 113, 87, 49, 17, 49, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 201, 200, 200, 115, 115, 87, 87, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 932
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043623 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043623
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043623/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043623
Building REAL250005043624
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043624'
/scratch/stefan/7916125/working/building/REAL250005043624 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043624

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043624/0 /scratch/stefan/7916125/working/building/REAL250005043624 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/733
`/scratch/stefan/7916125/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043624 none CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
249  conformations in input
total number of sets (complete confs): 249
using faster count positions algorithm for large data
unique positions, atoms: [24, 21, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 24, 24, 24, 24, 24, 24, 72, 21, 21, 1, 1, 1, 1, 30, 1, 1, 1, 1] 249
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 209
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043624 none CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
249  conformations in input
total number of sets (complete confs): 249
using faster count positions algorithm for large data
unique positions, atoms: [83, 82, 83, 83, 70, 30, 70, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 83, 83, 83, 83, 83, 83, 249, 82, 82, 30, 30, 30, 30, 1, 30, 30, 30, 30] 249
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 492
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043624 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043624
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043624/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043624
Building REAL250005043625
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043625'
/scratch/stefan/7916125/working/building/REAL250005043625 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043625

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043625/0 /scratch/stefan/7916125/working/building/REAL250005043625 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/734
`/scratch/stefan/7916125/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043625 none CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [35, 22, 34, 7, 22, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 35, 35, 35, 35, 35, 35, 35, 66, 1, 1, 1, 1, 27, 1, 1, 1, 1] 372
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 265
number of broken/clashed sets: 136
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043625 none CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [124, 113, 124, 81, 113, 113, 27, 81, 27, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 124, 124, 124, 124, 124, 124, 124, 339, 27, 27, 27, 27, 1, 27, 27, 27, 27] 372
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 780
number of broken/clashed sets: 136
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043625 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043625
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043625/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043625
Building REAL250005043626
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043626'
/scratch/stefan/7916125/working/building/REAL250005043626 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043626

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043626/0 /scratch/stefan/7916125/working/building/REAL250005043626 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/735
`/scratch/stefan/7916125/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043626 none CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [42, 22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 42, 42, 42, 42, 42, 22, 22, 22, 22, 1, 1, 1, 1, 36, 1, 1, 1, 1] 176
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 223
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043626 none CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [176, 122, 122, 122, 88, 36, 88, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 176, 176, 176, 176, 176, 122, 122, 122, 122, 36, 36, 36, 36, 1, 36, 36, 36, 36] 176
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 664
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043626 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043626
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043626/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043626
Building REAL250005043627
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043627'
/scratch/stefan/7916125/working/building/REAL250005043627 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043627

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043627/0 /scratch/stefan/7916125/working/building/REAL250005043627 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/736
`/scratch/stefan/7916125/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043627 none CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 6, 6, 6, 6, 1, 1, 1, 1, 29, 1, 1, 1, 1] 47
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043627 none CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 29, 47, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 1, 29, 29, 29, 29] 47
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043627 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043627
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043627/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043627
Building REAL250005043628
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043628'
/scratch/stefan/7916125/working/building/REAL250005043628 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043628

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043628/0 /scratch/stefan/7916125/working/building/REAL250005043628 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/737
`/scratch/stefan/7916125/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043628 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 37, 37, 55, 55, 55, 55, 55, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 55, 6, 6, 6, 6] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043628 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 29, 1, 1, 1, 1] 55
rigid atoms, others: [32, 1, 34, 33, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043628 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 29, 55, 55, 55, 55, 55, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 55, 55, 55, 55, 55, 29, 29, 29, 29, 1, 29, 29, 29, 29] 55
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 141
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043628 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043628
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043628/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043628
Building REAL250005043629
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043629'
/scratch/stefan/7916125/working/building/REAL250005043629 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043629

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043629/0 /scratch/stefan/7916125/working/building/REAL250005043629 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/738
`/scratch/stefan/7916125/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043629 none C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [66, 27, 66, 20, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 66, 66, 66, 66, 66, 27, 27, 20, 20, 1, 1, 1, 1, 33, 1, 1, 1, 1] 141
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 271
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043629 none C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 136, 91, 33, 91, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 141, 141, 141, 141, 141, 141, 141, 136, 136, 33, 33, 33, 33, 1, 33, 33, 33, 33] 141
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 473
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043629 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043629
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043629/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043629
Building REAL250005043630
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043630'
/scratch/stefan/7916125/working/building/REAL250005043630 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043630

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043630/0 /scratch/stefan/7916125/working/building/REAL250005043630 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/739
`/scratch/stefan/7916125/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043630 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 9, 9, 9, 9, 39, 39, 56, 56, 56, 56, 56, 9, 9, 1, 1, 2, 2, 2, 9, 9, 9, 9, 56, 9, 9, 9, 9, 1, 1, 1, 1] 56
rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043630 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 16, 1, 1, 1, 1, 9, 9, 9, 9] 56
rigid atoms, others: [2, 4, 5, 6, 7, 8, 16, 17, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 34, 3, 33, 35, 32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 27])
total number of confs: 51
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: REAL250005043630 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 16, 43, 16, 16, 16, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 56, 56, 56, 56, 56, 16, 16, 16, 16, 1, 16, 16, 16, 16, 56, 56, 56, 56] 56
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 160
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043630 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043630
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043630/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043630
Building REAL250005043631
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043631'
/scratch/stefan/7916125/working/building/REAL250005043631 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043631

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043631/0 /scratch/stefan/7916125/working/building/REAL250005043631 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/740
`/scratch/stefan/7916125/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1)

`REAL250005043631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043631 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 84, 84, 102, 102, 102, 102, 102, 33, 33, 1, 33, 33, 33, 33, 102, 102, 102, 102, 102, 102, 33, 33, 33, 33] 102
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 267
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043631 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 33, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 102
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29, 30, 31])
total number of confs: 105
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: REAL250005043631 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [76, 23, 76, 102, 102, 102, 102, 102, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 102, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 102
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 233
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043631 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043631
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043631/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043631
Building REAL250005043632
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043632'
/scratch/stefan/7916125/working/building/REAL250005043632 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043632

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043632/0 /scratch/stefan/7916125/working/building/REAL250005043632 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/741
`/scratch/stefan/7916125/working/3D/741' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043632 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 91, 91, 113, 113, 113, 113, 113, 33, 33, 1, 1, 33, 33, 33, 33, 113, 33, 33, 33, 33] 113
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043632 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 33, 33, 1, 1, 1, 1, 34, 1, 1, 1, 1] 113
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043632 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [87, 34, 87, 113, 113, 113, 113, 34, 34, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 113, 113, 34, 34, 34, 34, 1, 34, 34, 34, 34] 113
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 271
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043632 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043632
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043632/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043632
Building REAL250005043633
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043633'
/scratch/stefan/7916125/working/building/REAL250005043633 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043633

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043633/0 /scratch/stefan/7916125/working/building/REAL250005043633 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/742
`/scratch/stefan/7916125/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043633 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 28, 28, 60, 60, 60, 60, 176, 176, 201, 201, 201, 201, 201, 60, 60, 1, 1, 2, 2, 2, 7, 7, 60, 60, 60, 60, 201, 60, 60, 60, 60, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 493
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043633 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 60, 60, 60, 60, 60, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1, 60, 60, 60, 60] 201
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38])
total number of confs: 238
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: REAL250005043633 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 105, 33, 105, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 156, 156, 33, 33, 33, 33, 1, 33, 33, 33, 33, 201, 201, 201, 201] 201
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 678
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043633 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043633
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043633/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043633
Building REAL250005043634
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043634'
/scratch/stefan/7916125/working/building/REAL250005043634 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043634

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043634/0 /scratch/stefan/7916125/working/building/REAL250005043634 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/743
`/scratch/stefan/7916125/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043634 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 93, 93, 111, 111, 111, 111, 111, 33, 33, 1, 1, 33, 33, 33, 33, 111, 33, 33, 33, 33] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043634 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 33, 33, 1, 1, 1, 1, 33, 1, 1, 1, 1] 111
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043634 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [81, 33, 81, 111, 111, 111, 111, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 111, 111, 33, 33, 33, 33, 1, 33, 33, 33, 33] 111
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 249
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043634 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043634
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043634/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043634
Building REAL250005043635
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043635'
/scratch/stefan/7916125/working/building/REAL250005043635 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043635

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043635/0 /scratch/stefan/7916125/working/building/REAL250005043635 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/744
`/scratch/stefan/7916125/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043635 none C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 13, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 29, 1, 1, 1, 1] 54
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 77
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043635 none C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 52, 54, 54, 25, 54, 29, 29, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 54, 54, 54, 54, 54, 54, 54, 54, 54, 29, 29, 29, 29, 1, 29, 29, 29, 29] 54
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 160
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043635 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043635
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043635/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043635
Building REAL250005043636
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043636'
/scratch/stefan/7916125/working/building/REAL250005043636 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043636

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043636/0 /scratch/stefan/7916125/working/building/REAL250005043636 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/745
`/scratch/stefan/7916125/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043636 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 78, 78, 96, 96, 96, 96, 96, 24, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 96, 24, 24, 24, 24] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043636 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 31])
total number of confs: 105
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: REAL250005043636 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 73, 96, 31, 73, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 96, 96, 96, 96, 96, 31, 31, 31, 31, 1, 31, 31, 31, 31] 96
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 271
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043636 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043636
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043636/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043636
Building REAL250005043637
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043637'
/scratch/stefan/7916125/working/building/REAL250005043637 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043637

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043637/0 /scratch/stefan/7916125/working/building/REAL250005043637 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/746
`/scratch/stefan/7916125/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1)

`REAL250005043637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043637 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 5, 5, 5, 5, 21, 21, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 27
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 68
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043637 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 27
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 34
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: REAL250005043637 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 23, 11, 23, 11, 11, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 1, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 84
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043637 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043637
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043637/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043637
Building REAL250005043638
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043638'
/scratch/stefan/7916125/working/building/REAL250005043638 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043638

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043638/0 /scratch/stefan/7916125/working/building/REAL250005043638 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/747
`/scratch/stefan/7916125/working/3D/747' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043638 none CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 36, 36, 36, 36, 36, 22, 1, 1, 1, 1, 28, 1, 1, 1, 1] 130
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 210
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043638 none CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 126, 81, 126, 28, 81, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 130, 130, 130, 130, 130, 126, 28, 28, 28, 28, 1, 28, 28, 28, 28] 130
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 450
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043638 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043638
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043638/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043638
Building REAL250005043639
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043639'
/scratch/stefan/7916125/working/building/REAL250005043639 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043639

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043639/0 /scratch/stefan/7916125/working/building/REAL250005043639 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/748
`/scratch/stefan/7916125/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043639 none O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 30, 58, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 22, 22, 34, 34, 56, 56, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 317
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043639 none O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 95, 151, 201, 201, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 151, 151, 201, 201, 201, 201, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 799
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043639 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043639
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043639/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043639
Building REAL250005043640
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043640'
/scratch/stefan/7916125/working/building/REAL250005043640 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043640

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043640/0 /scratch/stefan/7916125/working/building/REAL250005043640 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/749
`/scratch/stefan/7916125/working/3D/749' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043640 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 78, 78, 96, 96, 96, 96, 96, 24, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 96, 24, 24, 24, 24] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043640 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 31])
total number of confs: 105
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: REAL250005043640 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 73, 96, 31, 73, 31, 31, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 96, 96, 96, 96, 96, 31, 31, 31, 31, 1, 31, 31, 31, 31] 96
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 286
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043640 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043640
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043640/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043640
Building REAL250005043641
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043641'
/scratch/stefan/7916125/working/building/REAL250005043641 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043641

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043641/0 /scratch/stefan/7916125/working/building/REAL250005043641 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/750
`/scratch/stefan/7916125/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043641 none CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [26, 17, 26, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 26, 26, 26, 26, 26, 26, 26, 17, 1, 1, 1, 1, 34, 1, 1, 1, 1] 116
rigid atoms, others: [32, 34, 35, 36, 5, 7, 8, 9, 10, 11, 37, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 158
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043641 none CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 98, 116, 82, 98, 34, 82, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 116, 116, 116, 116, 116, 116, 116, 98, 34, 34, 34, 34, 1, 34, 34, 34, 34] 116
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 389
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043641 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043641
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043641/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043641
Building REAL250005043642
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043642'
/scratch/stefan/7916125/working/building/REAL250005043642 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043642

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043642/0 /scratch/stefan/7916125/working/building/REAL250005043642 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/751
`/scratch/stefan/7916125/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043642 none C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 32, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 104, 104, 104, 59, 59, 34, 34, 18, 18, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 456
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043642 none C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 112, 79, 53, 15, 53, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 199, 199, 116, 116, 79, 79, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 918
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043642 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043642
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043642/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043642
Building REAL250005043643
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043643'
/scratch/stefan/7916125/working/building/REAL250005043643 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043643

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043643/0 /scratch/stefan/7916125/working/building/REAL250005043643 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/752
`/scratch/stefan/7916125/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043643 none CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 23, 1, 1, 1, 1] 114
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 103
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043643 none CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 112, 39, 112, 112, 23, 39, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 114, 114, 114, 114, 114, 112, 112, 112, 112, 112, 112, 23, 23, 23, 23, 1, 23, 23, 23, 23] 114
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 454
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043643 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043643
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043643/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043643
Building REAL250005043644
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043644'
/scratch/stefan/7916125/working/building/REAL250005043644 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043644

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043644/0 /scratch/stefan/7916125/working/building/REAL250005043644 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/753
`/scratch/stefan/7916125/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043644 none NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 29, 29, 1, 1, 1, 1, 27, 1, 1, 1, 1] 83
rigid atoms, others: [3, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 25])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043644 none NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 63, 83, 27, 63, 27, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 83, 83, 27, 27, 27, 27, 1, 27, 27, 27, 27] 83
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043644 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043644
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043644/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043644
Building REAL250005043645
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043645'
/scratch/stefan/7916125/working/building/REAL250005043645 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043645

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043645/0 /scratch/stefan/7916125/working/building/REAL250005043645 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/754
`/scratch/stefan/7916125/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043645 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 35, 35, 67, 67, 67, 67, 188, 188, 201, 201, 201, 201, 201, 67, 67, 2, 2, 2, 1, 1, 1, 1, 7, 7, 67, 67, 67, 67, 201, 67, 67, 67, 67] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 510
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043645 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 29, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 67, 67, 67, 67, 67, 67, 67, 29, 29, 1, 1, 1, 1, 24, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 259
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: REAL250005043645 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 159, 78, 24, 78, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 201, 201, 201, 201, 201, 201, 201, 159, 159, 24, 24, 24, 24, 1, 24, 24, 24, 24] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 724
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043645 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043645
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043645/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043645
Building REAL250005043646
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043646'
/scratch/stefan/7916125/working/building/REAL250005043646 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043646

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043646/0 /scratch/stefan/7916125/working/building/REAL250005043646 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/755
`/scratch/stefan/7916125/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043646 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 5, 5, 8, 8, 8, 8, 37, 37, 70, 70, 70, 70, 70, 8, 8, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 70, 8, 8, 8, 8, 1, 1, 1, 1] 80
rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043646 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 8, 8, 14, 14, 14, 14, 14, 1, 1, 1, 1, 24, 1, 1, 1, 1, 8, 8, 8, 8] 80
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043646 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 58, 24, 58, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 70, 70, 80, 80, 80, 80, 80, 24, 24, 24, 24, 1, 24, 24, 24, 24, 70, 70, 70, 70] 80
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043646 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043646
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043646/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043646
Building REAL250005043647
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043647'
/scratch/stefan/7916125/working/building/REAL250005043647 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043647

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043647/0 /scratch/stefan/7916125/working/building/REAL250005043647 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/756
`/scratch/stefan/7916125/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1)

`REAL250005043647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043647 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 64, 64, 73, 90, 73, 73, 23, 23, 1, 23, 23, 23, 23, 90, 90, 73, 73, 73, 73, 23, 23, 23, 23] 90
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 290
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043647 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 7, 7, 10, 34, 10, 10, 1, 1, 23, 1, 1, 1, 1, 34, 34, 10, 10, 10, 10, 1, 1, 1, 1] 90
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 153
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: REAL250005043647 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [42, 10, 42, 73, 73, 73, 73, 73, 10, 10, 10, 4, 1, 4, 1, 1, 10, 1, 1, 10, 10, 73, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 90
rigid atoms, others: [12, 14, 15, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 183
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043647 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043647
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043647/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043647
Building REAL250005043648
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043648'
/scratch/stefan/7916125/working/building/REAL250005043648 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043648

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043648/0 /scratch/stefan/7916125/working/building/REAL250005043648 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/757
`/scratch/stefan/7916125/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043648 none CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 12, 1, 1, 1, 1] 12
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 28
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043648 none CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12, 12, 12] 12
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 25
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043648 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043648
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043648/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043648
Building REAL250005043649
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043649'
/scratch/stefan/7916125/working/building/REAL250005043649 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043649

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043649/0 /scratch/stefan/7916125/working/building/REAL250005043649 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/758
`/scratch/stefan/7916125/working/3D/758' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043649 none CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 16, 31, 7, 16, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 1, 1, 1, 1, 31, 1, 1, 1, 1] 109
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 179
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043649 none CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 104, 109, 86, 104, 31, 86, 31, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 109, 109, 109, 109, 109, 109, 109, 104, 104, 104, 104, 31, 31, 31, 31, 1, 31, 31, 31, 31] 109
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 340
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043649 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043649
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043649/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043649
Building REAL250005043650
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043650'
/scratch/stefan/7916125/working/building/REAL250005043650 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043650

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043650/0 /scratch/stefan/7916125/working/building/REAL250005043650 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/759
`/scratch/stefan/7916125/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043650 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 30, 30, 30, 30, 108, 108, 186, 186, 186, 186, 186, 30, 30, 3, 3, 3, 3, 3, 1, 1, 30, 30, 30, 30, 186, 30, 30, 30, 30] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 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])
total number of confs: 385
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043650 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 30, 30, 30, 30, 6, 30, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 49, 49, 49, 49, 49, 30, 30, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 236
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: REAL250005043650 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 186, 186, 186, 115, 186, 36, 115, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 186, 186, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 618
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043650 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043650
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043650/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043650
Building REAL250005043651
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043651'
/scratch/stefan/7916125/working/building/REAL250005043651 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043651

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043651/0 /scratch/stefan/7916125/working/building/REAL250005043651 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/760
`/scratch/stefan/7916125/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1)

`REAL250005043651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043651 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 73, 73, 107, 107, 107, 107, 30, 30, 1, 30, 30, 30, 30, 107, 107, 107, 107, 107, 107, 107, 30, 30, 30, 30] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 305
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043651 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 1, 30, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1] 107
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 108
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: REAL250005043651 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [87, 26, 87, 107, 107, 107, 107, 107, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 26, 26, 107, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 107
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 251
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043651 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043651
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043651/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043651
Building REAL250005043652
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043652'
/scratch/stefan/7916125/working/building/REAL250005043652 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043652

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043652/0 /scratch/stefan/7916125/working/building/REAL250005043652 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/761
`/scratch/stefan/7916125/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CC(=O)N2)CC1)

`REAL250005043652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043652 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 35, 36, 36, 36, 85, 85, 112, 112, 112, 112, 112, 36, 36, 1, 36, 36, 36, 36, 112, 112, 112, 36, 36, 36, 36] 112
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 306
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043652 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 1, 1, 36, 1, 1, 1, 1, 24, 24, 24, 1, 1, 1, 1] 112
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29])
total number of confs: 110
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: REAL250005043652 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [83, 24, 83, 112, 112, 112, 112, 112, 24, 24, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 24, 24, 112, 24, 24, 24, 24, 1, 1, 1, 24, 24, 24, 24] 112
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 261
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043652 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043652
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043652/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043652
Building REAL250005043653
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043653'
/scratch/stefan/7916125/working/building/REAL250005043653 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043653

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043653/0 /scratch/stefan/7916125/working/building/REAL250005043653 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/762
`/scratch/stefan/7916125/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CC(=O)N2)CC1)

`REAL250005043653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043653 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 90, 90, 111, 111, 111, 111, 111, 37, 37, 1, 37, 37, 37, 37, 111, 111, 111, 37, 37, 37, 37] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 291
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043653 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 1, 1, 37, 1, 1, 1, 1, 25, 25, 25, 1, 1, 1, 1] 111
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29])
total number of confs: 113
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: REAL250005043653 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CC(=O)N2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [83, 25, 83, 111, 111, 111, 111, 111, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 25, 25, 111, 25, 25, 25, 25, 1, 1, 1, 25, 25, 25, 25] 111
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33])
total number of confs: 251
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043653 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043653
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043653/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043653
Building REAL250005043654
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043654'
/scratch/stefan/7916125/working/building/REAL250005043654 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043654

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043654/0 /scratch/stefan/7916125/working/building/REAL250005043654 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/763
`/scratch/stefan/7916125/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043654 none COC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 7, 7, 17, 17, 17, 16, 62, 62, 93, 93, 93, 93, 93, 17, 17, 1, 1, 5, 5, 5, 17, 17, 17, 17, 93, 17, 17, 17, 17, 1, 1, 1, 1] 93
rigid atoms, others: [1, 2, 3, 36, 35, 33, 34, 19, 20] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 213
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043654 none COC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 17, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 17, 17, 21, 21, 21, 1, 1, 1, 1, 37, 1, 1, 1, 1, 17, 17, 17, 17] 93
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 34, 4, 35, 33, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 36, 28])
total number of confs: 104
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043654 none COC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 37, 73, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 37, 93, 93, 93, 93, 93, 37, 37, 37, 37, 1, 37, 37, 37, 37, 93, 93, 93, 93] 93
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 266
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043654 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043654
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043654/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043654
Building REAL250005043655
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043655'
/scratch/stefan/7916125/working/building/REAL250005043655 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043655

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043655/0 /scratch/stefan/7916125/working/building/REAL250005043655 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/764
`/scratch/stefan/7916125/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CSC2)CC1)

`REAL250005043655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043655 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 31, 66, 66, 97, 97, 97, 31, 31, 1, 31, 31, 31, 31, 97, 97, 97, 97, 97, 31, 31, 31, 31] 97
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 285
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043655 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 1, 1, 31, 1, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 1, 1] 97
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 99
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: REAL250005043655 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CSC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 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
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [73, 21, 73, 97, 97, 97, 97, 97, 21, 21, 20, 6, 1, 6, 1, 1, 1, 1, 21, 21, 97, 21, 21, 21, 21, 1, 1, 1, 1, 1, 21, 21, 21, 21] 97
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33])
total number of confs: 223
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043655 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043655
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043655/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043655
Building REAL250005043656
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043656'
/scratch/stefan/7916125/working/building/REAL250005043656 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043656

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043656/0 /scratch/stefan/7916125/working/building/REAL250005043656 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/765
`/scratch/stefan/7916125/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043656 none C=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [78, 26, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 78, 78, 78, 26, 26, 1, 1, 1, 1, 30, 1, 1, 1, 1] 168
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 276
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043656 none C=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 168, 110, 30, 110, 30, 30, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 30, 30, 168, 168, 168, 168, 168, 30, 30, 30, 30, 1, 30, 30, 30, 30] 168
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 568
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043656 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043656
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043656/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043656
Building REAL250005043657
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043657'
/scratch/stefan/7916125/working/building/REAL250005043657 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043657

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043657/0 /scratch/stefan/7916125/working/building/REAL250005043657 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/766
`/scratch/stefan/7916125/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043657 none C[NH+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 19, 1, 1, 1, 1] 78
rigid atoms, others: [32, 34, 35, 36, 5, 7, 8, 9, 10, 11, 37, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 120
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043657 none C[NH+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 78, 78, 78, 43, 19, 43, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 78, 78, 78, 78, 78, 78, 78, 78, 19, 19, 19, 19, 1, 19, 19, 19, 19] 78
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 270
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043657 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043657/1 /scratch/stefan/7916125/working/building/REAL250005043657 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/767
`/scratch/stefan/7916125/working/3D/767' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043657.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043657/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043657 none CN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [56, 29, 56, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 42, 42, 42, 42, 42, 1, 1, 56, 56, 56, 56, 56, 56, 29, 29, 1, 1, 1, 1, 42, 1, 1, 1, 1] 188
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 32, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 251
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043657 none CN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
188  conformations in input
total number of sets (complete confs): 188
using faster count positions algorithm for large data
unique positions, atoms: [188, 172, 188, 127, 42, 127, 42, 42, 42, 12, 1, 12, 1, 1, 1, 1, 1, 1, 41, 42, 188, 188, 188, 188, 188, 188, 172, 172, 42, 42, 42, 42, 1, 42, 42, 42, 42] 188
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 622
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043657 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043657
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043657/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043657/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043657
Building REAL250005043658
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043658'
/scratch/stefan/7916125/working/building/REAL250005043658 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043658

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043658/0 /scratch/stefan/7916125/working/building/REAL250005043658 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/768
`/scratch/stefan/7916125/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043658 none C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
510  conformations in input
total number of sets (complete confs): 510
using faster count positions algorithm for large data
unique positions, atoms: [63, 22, 6, 22, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 63, 63, 63, 22, 66, 1, 1, 1, 1, 33, 1, 1, 1, 1] 510
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 309
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043658 none C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
510  conformations in input
total number of sets (complete confs): 510
using faster count positions algorithm for large data
unique positions, atoms: [170, 170, 106, 170, 33, 106, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 170, 170, 170, 170, 510, 33, 33, 33, 33, 1, 33, 33, 33, 33] 510
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 1105
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043658 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043658
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043658/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043658
Building REAL250005043659
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043659'
/scratch/stefan/7916125/working/building/REAL250005043659 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043659

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043659/0 /scratch/stefan/7916125/working/building/REAL250005043659 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/769
`/scratch/stefan/7916125/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1)

`REAL250005043659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043659 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 30, 68, 68, 92, 92, 92, 30, 30, 1, 30, 30, 30, 30, 92, 92, 92, 92, 92, 30, 30, 30, 30] 92
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043659 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 1, 30, 1, 1, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1] 92
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043659 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [72, 19, 72, 92, 92, 92, 92, 92, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 19, 19, 92, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 19, 19] 92
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33])
total number of confs: 215
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043659 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043659
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043659/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043659
Building REAL250005043660
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043660'
/scratch/stefan/7916125/working/building/REAL250005043660 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043660

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043660/0 /scratch/stefan/7916125/working/building/REAL250005043660 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/770
`/scratch/stefan/7916125/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043660 none CO[C@H](C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [34, 21, 7, 21, 21, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 34, 34, 34, 21, 21, 21, 1, 1, 1, 1, 35, 1, 1, 1, 1] 116
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 145
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043660 none CO[C@H](C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 113, 96, 113, 113, 35, 96, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 35, 116, 116, 116, 113, 113, 113, 35, 35, 35, 35, 1, 35, 35, 35, 35] 116
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 343
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043660 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043660
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043660/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043660
Building REAL250005043661
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043661'
/scratch/stefan/7916125/working/building/REAL250005043661 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043661

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043661/0 /scratch/stefan/7916125/working/building/REAL250005043661 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/771
`/scratch/stefan/7916125/working/3D/771' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043661 none CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 70, 70, 70, 70, 70, 24, 72, 1, 1, 1, 1, 28, 1, 1, 1, 1] 603
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 328
number of broken/clashed sets: 166
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043661 none CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 177, 92, 177, 28, 92, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 201, 201, 201, 177, 531, 28, 28, 28, 28, 1, 28, 28, 28, 28] 603
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1282
number of broken/clashed sets: 166
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043661 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043661
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043661/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043661
Building REAL250005043662
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043662'
/scratch/stefan/7916125/working/building/REAL250005043662 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043662

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043662/0 /scratch/stefan/7916125/working/building/REAL250005043662 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/772
`/scratch/stefan/7916125/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C)

`REAL250005043662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043662 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 12, 15, 15, 15, 12, 12, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 39
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 89
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043662 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [36, 33, 36, 16, 33, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 36, 39, 39, 39, 36, 36, 36, 16, 16, 16, 16, 1, 16, 16, 16, 16, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 117
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043662 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043662/1 /scratch/stefan/7916125/working/building/REAL250005043662 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/773
`/scratch/stefan/7916125/working/3D/773' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C)

`REAL250005043662.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043662/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043662 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 19, 33, 33, 19, 19, 19, 1, 1, 1, 1, 34, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33] 112
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 166
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043662 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [111, 95, 111, 34, 95, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 111, 112, 112, 111, 111, 111, 34, 34, 34, 34, 1, 34, 34, 34, 34, 112, 112, 112, 112, 112, 112] 112
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 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: 323
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043662 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043662
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043662/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043662/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043662
Building REAL250005043663
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043663'
/scratch/stefan/7916125/working/building/REAL250005043663 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043663

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043663/0 /scratch/stefan/7916125/working/building/REAL250005043663 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/774
`/scratch/stefan/7916125/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043663 none CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 39, 7, 39, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 71, 71, 71, 71, 71, 39, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043663 none CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 99, 163, 27, 99, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 163, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 675
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043663 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043663
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043663/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043663
Building REAL250005043664
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043664'
/scratch/stefan/7916125/working/building/REAL250005043664 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043664

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043664/0 /scratch/stefan/7916125/working/building/REAL250005043664 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/775
`/scratch/stefan/7916125/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043664 none CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 31, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 59, 59, 59, 59, 59, 31, 31, 1, 1, 1, 1, 37, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 269
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043664 none CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 177, 120, 37, 120, 37, 37, 37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 177, 177, 37, 37, 37, 37, 1, 37, 37, 37, 37] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 623
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043664 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043664
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043664/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043664
Building REAL250005043665
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043665'
/scratch/stefan/7916125/working/building/REAL250005043665 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL250005043665 as failed and skipping
/scratch/stefan/7916125/working /scratch/stefan/7916125
`/scratch/stefan/7916125/working/building/REAL250005043665' -> `/scratch/stefan/7916125/failed/REAL250005043665'
Building REAL250005043666
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043666'
/scratch/stefan/7916125/working/building/REAL250005043666 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043666

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043666/0 /scratch/stefan/7916125/working/building/REAL250005043666 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/776
`/scratch/stefan/7916125/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043666 none CC(C)(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
216  conformations in input
total number of sets (complete confs): 216
using faster count positions algorithm for large data
unique positions, atoms: [7, 3, 7, 7, 11, 1, 3, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 33, 1, 1, 1, 1, 27, 1, 1, 1, 1] 216
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 122
number of broken/clashed sets: 216
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043666 none CC(C)(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
216  conformations in input
total number of sets (complete confs): 216
using faster count positions algorithm for large data
unique positions, atoms: [72, 45, 72, 72, 72, 27, 45, 27, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 72, 72, 72, 72, 72, 72, 72, 71, 216, 27, 27, 27, 27, 1, 27, 27, 27, 27] 216
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 468
number of broken/clashed sets: 216
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043666 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043666
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043666/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043666
Building REAL250005043667
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043667'
/scratch/stefan/7916125/working/building/REAL250005043667 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043667

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043667/0 /scratch/stefan/7916125/working/building/REAL250005043667 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/777
`/scratch/stefan/7916125/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CCC2)CC1)

`REAL250005043667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043667 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 35, 73, 73, 95, 95, 95, 95, 35, 35, 1, 35, 35, 35, 35, 95, 95, 95, 95, 95, 95, 35, 35, 35, 35] 95
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043667 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 1, 1, 35, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1] 95
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043667 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [62, 19, 62, 95, 95, 95, 95, 95, 19, 19, 19, 7, 1, 7, 1, 1, 1, 1, 1, 19, 19, 95, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 95
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35])
total number of confs: 211
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043667 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043667
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043667/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043667
Building REAL250005043668
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043668'
/scratch/stefan/7916125/working/building/REAL250005043668 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043668

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043668/0 /scratch/stefan/7916125/working/building/REAL250005043668 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/778
`/scratch/stefan/7916125/working/3D/778' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043668 none O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 21, 21, 63, 1, 1, 1, 1, 34, 1, 1, 1, 1] 255
rigid atoms, others: [1, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 26, 27, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 25])
total number of confs: 186
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043668 none O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [64, 34, 64, 85, 34, 34, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 85, 85, 255, 34, 34, 34, 34, 1, 34, 34, 34, 34] 255
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 544
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043668 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043668
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043668/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043668
Building REAL250005043669
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043669'
/scratch/stefan/7916125/working/building/REAL250005043669 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043669

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043669/0 /scratch/stefan/7916125/working/building/REAL250005043669 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/779
`/scratch/stefan/7916125/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043669 none NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 94, 35, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 94, 94, 35, 35, 1, 1, 1, 1, 28, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 294
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043669 none NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 185, 201, 185, 99, 28, 99, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 185, 185, 28, 28, 28, 28, 1, 28, 28, 28, 28] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 596
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043669 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043669
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043669/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043669
Building REAL250005043670
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043670'
/scratch/stefan/7916125/working/building/REAL250005043670 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043670

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043670/0 /scratch/stefan/7916125/working/building/REAL250005043670 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/780
`/scratch/stefan/7916125/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043670 none CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 18, 18, 18, 18, 54, 1, 1, 1, 1, 25, 1, 1, 1, 1] 210
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 155
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043670 none CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [70, 59, 70, 25, 59, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 70, 70, 70, 70, 210, 25, 25, 25, 25, 1, 25, 25, 25, 25] 210
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 419
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043670 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043670
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043670/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043670
Building REAL250005043671
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043671'
/scratch/stefan/7916125/working/building/REAL250005043671 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043671

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043671/0 /scratch/stefan/7916125/working/building/REAL250005043671 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/781
`/scratch/stefan/7916125/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CCC2)CC1)

`REAL250005043671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043671 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
237  conformations in input
total number of sets (complete confs): 237
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 61, 61, 79, 79, 79, 79, 30, 30, 1, 30, 30, 30, 30, 237, 79, 79, 79, 79, 79, 79, 30, 30, 30, 30] 237
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 449
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043671 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
237  conformations in input
total number of sets (complete confs): 237
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 1, 1, 30, 1, 1, 1, 1, 45, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 237
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 127
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: REAL250005043671 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
237  conformations in input
total number of sets (complete confs): 237
using faster count positions algorithm for large data
unique positions, atoms: [59, 15, 59, 79, 79, 79, 79, 79, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 15, 15, 79, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 237
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 187
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043671 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043671
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043671/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043671
Building REAL250005043672
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043672'
/scratch/stefan/7916125/working/building/REAL250005043672 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043672

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043672/0 /scratch/stefan/7916125/working/building/REAL250005043672 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/782
`/scratch/stefan/7916125/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C(O)C2CC2)CC1)

`REAL250005043672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043672 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C(O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 103, 103, 165, 165, 201, 201, 33, 33, 1, 33, 33, 33, 33, 165, 495, 201, 201, 201, 201, 201, 33, 33, 33, 33] 603
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 1205
number of broken/clashed sets: 153
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043672 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C(O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 6, 25, 25, 61, 61, 1, 1, 33, 1, 1, 1, 1, 25, 75, 61, 61, 61, 61, 61, 1, 1, 1, 1] 603
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 319
number of broken/clashed sets: 153
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043672 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C(O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [167, 61, 167, 201, 201, 201, 201, 201, 61, 61, 61, 29, 7, 29, 1, 7, 1, 1, 1, 61, 61, 201, 61, 61, 61, 61, 7, 21, 1, 1, 1, 1, 1, 61, 61, 61, 61] 603
rigid atoms, others: [32, 14, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 504
number of broken/clashed sets: 153
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043672 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043672
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043672/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043672
Building REAL250005043673
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043673'
/scratch/stefan/7916125/working/building/REAL250005043673 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043673

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043673/0 /scratch/stefan/7916125/working/building/REAL250005043673 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/783
`/scratch/stefan/7916125/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043673 none C=CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 57, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 93, 93, 93, 57, 57, 19, 19, 19, 19, 1, 1, 1, 1, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 377
number of broken/clashed sets: 101
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043673 none C=CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 143, 82, 143, 21, 82, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 143, 143, 143, 143, 21, 21, 21, 21, 1, 21, 21, 21, 21] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 847
number of broken/clashed sets: 101
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043673 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043673
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043673/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043673
Building REAL250005043674
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043674'
/scratch/stefan/7916125/working/building/REAL250005043674 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043674

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043674/0 /scratch/stefan/7916125/working/building/REAL250005043674 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/784
`/scratch/stefan/7916125/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2F)CC1)

`REAL250005043674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043674 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 63, 63, 77, 77, 77, 30, 30, 1, 30, 30, 30, 30, 77, 77, 77, 77, 30, 30, 30, 30] 77
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 199
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043674 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 1, 1, 30, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 1] 77
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28])
total number of confs: 96
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043674 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
77  conformations in input
total number of sets (complete confs): 77
using faster count positions algorithm for large data
unique positions, atoms: [61, 20, 61, 77, 77, 77, 77, 77, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 20, 20, 77, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 77
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 182
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043674 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043674
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043674/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043674
Building REAL250005043675
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043675'
/scratch/stefan/7916125/working/building/REAL250005043675 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043675

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043675/0 /scratch/stefan/7916125/working/building/REAL250005043675 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/785
`/scratch/stefan/7916125/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C)

`REAL250005043675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043675 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 12, 15, 15, 15, 12, 12, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 39
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 89
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043675 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [36, 33, 36, 16, 33, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 36, 39, 39, 39, 36, 36, 36, 16, 16, 16, 16, 1, 16, 16, 16, 16, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 117
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043675 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043675/1 /scratch/stefan/7916125/working/building/REAL250005043675 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/786
`/scratch/stefan/7916125/working/3D/786' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C)

`REAL250005043675.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043675/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043675 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 19, 33, 33, 19, 19, 19, 1, 1, 1, 1, 34, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33] 112
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 166
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043675 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [111, 95, 111, 34, 95, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 111, 112, 112, 111, 111, 111, 34, 34, 34, 34, 1, 34, 34, 34, 34, 112, 112, 112, 112, 112, 112] 112
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 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: 323
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043675 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043675
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043675/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043675/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043675
Building REAL250005043676
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043676'
/scratch/stefan/7916125/working/building/REAL250005043676 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043676

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043676/0 /scratch/stefan/7916125/working/building/REAL250005043676 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/787
`/scratch/stefan/7916125/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043676 none O=C(CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 46, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 22, 22, 46, 46, 1, 1, 1, 1, 27, 1, 1, 1, 1] 131
rigid atoms, others: [1, 5, 6, 7, 8, 9, 17, 18, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 27])
total number of confs: 239
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043676 none O=C(CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [87, 27, 87, 129, 131, 27, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 129, 129, 131, 131, 27, 27, 27, 27, 1, 27, 27, 27, 27] 131
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 449
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043676 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043676
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043676/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043676
Building REAL250005043677
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043677'
/scratch/stefan/7916125/working/building/REAL250005043677 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043677

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043677/0 /scratch/stefan/7916125/working/building/REAL250005043677 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/788
`/scratch/stefan/7916125/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)COC2)CC1)

`REAL250005043677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043677 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
216  conformations in input
total number of sets (complete confs): 216
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 27, 27, 27, 27, 63, 63, 72, 72, 72, 72, 27, 27, 1, 27, 27, 27, 27, 216, 72, 72, 72, 72, 27, 27, 27, 27] 216
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 408
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043677 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
216  conformations in input
total number of sets (complete confs): 216
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 1, 1, 27, 1, 1, 1, 1, 45, 15, 15, 15, 15, 1, 1, 1, 1] 216
rigid atoms, others: [32, 1, 34, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30])
total number of confs: 126
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: REAL250005043677 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
216  conformations in input
total number of sets (complete confs): 216
using faster count positions algorithm for large data
unique positions, atoms: [53, 15, 53, 72, 72, 72, 72, 72, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 15, 15, 72, 15, 15, 15, 15, 6, 1, 1, 1, 1, 15, 15, 15, 15] 216
rigid atoms, others: [12, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34])
total number of confs: 174
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043677 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043677
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043677/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043677
Building REAL250005043678
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043678'
/scratch/stefan/7916125/working/building/REAL250005043678 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043678

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043678/0 /scratch/stefan/7916125/working/building/REAL250005043678 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/789
`/scratch/stefan/7916125/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)=C1CC1)

`REAL250005043678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043678 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 33, 1, 1, 1, 1, 22, 22, 22, 22] 104
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 103
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043678 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [104, 76, 33, 76, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 104, 104, 104, 104, 104, 104, 33, 33, 33, 33, 1, 33, 33, 33, 33, 104, 104, 104, 104] 104
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 293
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043678 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)=C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
104  conformations in input
total number of sets (complete confs): 104
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 10, 10, 22, 22, 22, 22, 80, 80, 104, 104, 104, 104, 104, 22, 22, 1, 1, 1, 2, 2, 2, 22, 22, 22, 22, 104, 22, 22, 22, 22, 1, 1, 1, 1] 104
rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 245
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043678 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043678
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043678/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043678
Building REAL250005043679
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043679'
/scratch/stefan/7916125/working/building/REAL250005043679 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043679

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043679/0 /scratch/stefan/7916125/working/building/REAL250005043679 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/790
`/scratch/stefan/7916125/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043679 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 74, 74, 91, 91, 91, 91, 91, 25, 25, 2, 2, 2, 2, 2, 1, 1, 1, 1, 25, 25, 25, 25, 91, 25, 25, 25, 25] 91
rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 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])
total number of confs: 211
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043679 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 25, 1, 1, 1, 1] 91
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 101
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: REAL250005043679 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 25, 73, 25, 25, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 91, 91, 91, 91, 91, 91, 91, 91, 91, 25, 25, 25, 25, 1, 25, 25, 25, 25] 91
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043679 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043679
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043679/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043679
Building REAL250005043680
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043680'
/scratch/stefan/7916125/working/building/REAL250005043680 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043680

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043680/0 /scratch/stefan/7916125/working/building/REAL250005043680 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/791
`/scratch/stefan/7916125/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1(O)CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043680 none O=C(CC1(O)CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 8, 1, 1, 1, 1, 1, 29, 60, 60, 60, 60, 175, 175, 201, 201, 201, 201, 201, 60, 60, 8, 8, 6, 1, 1, 1, 1, 60, 60, 60, 60, 201, 60, 60, 60, 60] 603
rigid atoms, others: [2, 3, 4, 5, 6, 24, 25, 26, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 504
number of broken/clashed sets: 194
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043680 none O=C(CC1(O)CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 28, 60, 60, 60, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 28, 28, 180, 60, 60, 60, 60, 1, 1, 1, 1, 28, 1, 1, 1, 1] 603
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 428
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: REAL250005043680 none O=C(CC1(O)CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [96, 28, 98, 186, 201, 201, 201, 28, 28, 28, 9, 1, 9, 1, 1, 1, 1, 1, 1, 28, 28, 186, 186, 603, 201, 201, 201, 201, 28, 28, 28, 28, 1, 28, 28, 28, 28] 603
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1319
number of broken/clashed sets: 194
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043680 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043680
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043680/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043680
Building REAL250005043681
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043681'
/scratch/stefan/7916125/working/building/REAL250005043681 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043681

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043681/0 /scratch/stefan/7916125/working/building/REAL250005043681 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/792
`/scratch/stefan/7916125/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043681 none O=C(C=CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 29, 29, 91, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 29, 29, 91, 91, 1, 1, 1, 1, 38, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 371
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043681 none O=C(C=CCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 114, 187, 187, 201, 38, 38, 38, 11, 1, 11, 1, 1, 1, 1, 1, 1, 38, 38, 187, 187, 201, 201, 38, 38, 38, 38, 1, 38, 38, 38, 38] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 613
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043681 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043681
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043681/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043681
Building REAL250005043682
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043682'
/scratch/stefan/7916125/working/building/REAL250005043682 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043682

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043682/0 /scratch/stefan/7916125/working/building/REAL250005043682 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/793
`/scratch/stefan/7916125/working/3D/793' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043682.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043682.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043682/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043682 none C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 40, 40, 40, 27, 27, 1, 1, 1, 1, 25, 1, 1, 1, 1] 164
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 204
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043682 none C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 146, 87, 25, 87, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 164, 164, 164, 146, 146, 25, 25, 25, 25, 1, 25, 25, 25, 25] 164
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 619
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043682 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043682
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043682/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043682
Building REAL250005043683
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043683'
/scratch/stefan/7916125/working/building/REAL250005043683 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043683

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043683/0 /scratch/stefan/7916125/working/building/REAL250005043683 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/794
`/scratch/stefan/7916125/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043683 none O=C(CN1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 1, 1, 1, 1, 1, 28, 63, 63, 63, 63, 163, 163, 201, 201, 201, 201, 201, 63, 63, 6, 6, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 201, 63, 63, 63, 63] 201
rigid atoms, others: [2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 480
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043683 none O=C(CN1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 63, 63, 63, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 32, 32, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 40, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
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: REAL250005043683 none O=C(CN1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 40, 126, 182, 201, 201, 201, 40, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 182, 182, 201, 201, 201, 201, 201, 201, 40, 40, 40, 40, 1, 40, 40, 40, 40] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 634
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043683 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043683/1 /scratch/stefan/7916125/working/building/REAL250005043683 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/795
`/scratch/stefan/7916125/working/3D/795' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C[NH+]1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043683.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043683/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043683 none O=C(C[NH+]1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 9, 6, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 5, 1, 1, 1, 1, 1, 1, 12, 22, 22, 22, 22, 64, 64, 66, 66, 66, 66, 66, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 66, 22, 22, 22, 22] 66
rigid atoms, others: [2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 184
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043683 none O=C(C[NH+]1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 9, 6, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 6, 7, 22, 22, 22, 22, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 7, 7, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 20, 1, 1, 1, 1] 66
rigid atoms, others: [32, 1, 35, 36, 37, 38, 33, 8, 9, 10, 11, 12, 20, 21, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043683 none O=C(C[NH+]1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 9, 6, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 20, 44, 44, 66, 66, 66, 66, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 44, 44, 66, 66, 66, 66, 66, 66, 20, 20, 20, 20, 1, 20, 20, 20, 20] 66
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 198
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043683 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043683
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043683/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043683/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043683
Building REAL250005043684
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043684'
/scratch/stefan/7916125/working/building/REAL250005043684 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043684

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043684/0 /scratch/stefan/7916125/working/building/REAL250005043684 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/796
`/scratch/stefan/7916125/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043684 none C#C[C@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 17, 17, 17, 59, 59, 76, 76, 76, 76, 76, 17, 17, 1, 1, 1, 17, 17, 17, 17, 76, 17, 17, 17, 17] 76
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 174
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043684 none C#C[C@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 17, 17, 17, 1, 1, 1, 1, 26, 1, 1, 1, 1] 76
rigid atoms, others: [32, 33, 34, 7, 9, 10, 11, 12, 13, 21, 22, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 30])
total number of confs: 86
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: REAL250005043684 none C#C[C@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
76  conformations in input
total number of sets (complete confs): 76
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 76, 76, 70, 76, 26, 70, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 76, 76, 76, 26, 26, 26, 26, 1, 26, 26, 26, 26] 76
rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 194
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043684 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043684
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043684/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043684
Building REAL250005043685
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043685'
/scratch/stefan/7916125/working/building/REAL250005043685 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043685

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043685/0 /scratch/stefan/7916125/working/building/REAL250005043685 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/797
`/scratch/stefan/7916125/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1)

`REAL250005043685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043685 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 35, 83, 83, 103, 103, 103, 103, 35, 34, 1, 35, 35, 35, 35, 103, 103, 103, 103, 103, 103, 103, 35, 35, 35, 35] 103
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 282
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043685 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 1, 1, 35, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1] 103
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 115
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: REAL250005043685 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [81, 27, 81, 103, 103, 103, 103, 103, 27, 27, 27, 8, 1, 8, 1, 1, 1, 1, 1, 27, 27, 103, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 103
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 231
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043685 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043685
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043685/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043685
Building REAL250005043686
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043686'
/scratch/stefan/7916125/working/building/REAL250005043686 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043686

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043686/0 /scratch/stefan/7916125/working/building/REAL250005043686 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/798
`/scratch/stefan/7916125/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043686 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 81, 81, 105, 105, 105, 105, 105, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 105, 24, 24, 24, 24] 105
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 240
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043686 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 36, 1, 1, 1, 1] 105
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 110
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: REAL250005043686 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 105, 85, 36, 85, 36, 36, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 105, 105, 105, 105, 105, 105, 105, 36, 36, 36, 36, 1, 36, 36, 36, 36] 105
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043686 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043686
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043686/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043686
Building REAL250005043687
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043687'
/scratch/stefan/7916125/working/building/REAL250005043687 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043687

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043687/0 /scratch/stefan/7916125/working/building/REAL250005043687 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/799
`/scratch/stefan/7916125/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C)

`REAL250005043687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043687 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 31, 31, 45, 45, 45, 45, 45, 7, 7, 1, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 45, 7, 7, 7, 7, 2, 2, 2] 45
rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043687 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 26, 1, 1, 1, 1, 7, 7, 7] 45
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31, 36, 37, 38])
total number of confs: 56
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043687 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 42, 26, 42, 26, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45, 26, 26, 26, 26, 1, 26, 26, 26, 26, 45, 45, 45] 45
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043687 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043687
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043687/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043687
Building REAL250005043688
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043688'
/scratch/stefan/7916125/working/building/REAL250005043688 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043688

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043688/0 /scratch/stefan/7916125/working/building/REAL250005043688 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/800
`/scratch/stefan/7916125/working/3D/800' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C)

`REAL250005043688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043688 none C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 12, 16, 16, 16, 12, 12, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16] 39
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 95
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043688 none C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [36, 33, 36, 16, 33, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 36, 39, 39, 39, 36, 36, 36, 16, 16, 16, 16, 1, 16, 16, 16, 16, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 117
number of broken/clashed sets: 35
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043688 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043688/1 /scratch/stefan/7916125/working/building/REAL250005043688 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/801
`/scratch/stefan/7916125/working/3D/801' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C)

`REAL250005043688.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043688/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043688 none C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 18, 35, 35, 18, 18, 18, 1, 1, 1, 1, 33, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35] 117
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 166
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043688 none C[C@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
117  conformations in input
total number of sets (complete confs): 117
using faster count positions algorithm for large data
unique positions, atoms: [115, 93, 115, 33, 93, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 115, 117, 117, 115, 115, 115, 33, 33, 33, 33, 1, 33, 33, 33, 33, 117, 117, 117, 117, 117, 117] 117
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 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: 362
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043688 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043688
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043688/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043688/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043688
Building REAL250005043689
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043689'
/scratch/stefan/7916125/working/building/REAL250005043689 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043689

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043689/0 /scratch/stefan/7916125/working/building/REAL250005043689 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/802
`/scratch/stefan/7916125/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043689 none CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 68, 68, 68, 68, 68, 43, 43, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 232
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043689 none CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 121, 36, 121, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 185, 185, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 584
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043689 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043689
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043689/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043689
Building REAL250005043690
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043690'
/scratch/stefan/7916125/working/building/REAL250005043690 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043690

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043690/0 /scratch/stefan/7916125/working/building/REAL250005043690 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/803
`/scratch/stefan/7916125/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043690 none COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 81, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 121, 121, 121, 81, 81, 21, 21, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 386
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043690 none COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 107, 107, 57, 13, 57, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 192, 192, 107, 107, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 734
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043690 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043690
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043690/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043690
Building REAL250005043691
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043691'
/scratch/stefan/7916125/working/building/REAL250005043691 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043691

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043691/0 /scratch/stefan/7916125/working/building/REAL250005043691 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/804
`/scratch/stefan/7916125/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)COC1)

`REAL250005043691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043691 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 7, 7, 7, 7, 27, 27, 42, 42, 42, 42, 42, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 42, 7, 7, 7, 7, 1, 1, 1, 1] 42
rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 95
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043691 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 7, 7, 7, 7] 42
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 34, 3, 36, 35, 33, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 43
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: REAL250005043691 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
42  conformations in input
total number of sets (complete confs): 42
using default count positions algorithm for smaller data
unique positions, atoms: [42, 42, 16, 42, 16, 16, 16, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 42, 42, 42, 42, 42, 42, 16, 16, 16, 16, 1, 16, 16, 16, 16, 42, 42, 42, 42] 42
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 104
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043691 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043691
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043691/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043691
Building REAL250005043692
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043692'
/scratch/stefan/7916125/working/building/REAL250005043692 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043692

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043692/0 /scratch/stefan/7916125/working/building/REAL250005043692 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/805
`/scratch/stefan/7916125/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1)

`REAL250005043692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043692 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 20, 66, 67, 89, 89, 89, 22, 22, 1, 22, 22, 22, 22, 89, 89, 89, 89, 89, 22, 22, 22, 22] 89
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 261
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043692 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 22, 1, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1] 89
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 94
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: REAL250005043692 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [76, 23, 76, 89, 89, 89, 89, 89, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 23, 89, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23] 89
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33])
total number of confs: 207
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043692 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043692
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043692/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043692
Building REAL250005043693
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043693'
/scratch/stefan/7916125/working/building/REAL250005043693 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043693

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043693/0 /scratch/stefan/7916125/working/building/REAL250005043693 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/806
`/scratch/stefan/7916125/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043693 none [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 26, 26, 16, 16, 1, 1, 1, 1, 25, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 217
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043693 none [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 100, 81, 25, 81, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 125, 125, 100, 100, 25, 25, 25, 25, 1, 25, 25, 25, 25] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 568
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043693 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043693
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043693/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043693
Building REAL250005043694
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043694'
/scratch/stefan/7916125/working/building/REAL250005043694 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043694

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043694/0 /scratch/stefan/7916125/working/building/REAL250005043694 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/807
`/scratch/stefan/7916125/working/3D/807' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043694 none C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 53, 20, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 101, 101, 101, 20, 20, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043694 none C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 140, 90, 45, 13, 45, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 90, 90, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043694 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043694
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043694/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043694
Building REAL250005043695
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043695'
/scratch/stefan/7916125/working/building/REAL250005043695 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043695

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043695/0 /scratch/stefan/7916125/working/building/REAL250005043695 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/808
`/scratch/stefan/7916125/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043695 none CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 9, 9, 9, 9, 9, 9, 27, 1, 1, 1, 1, 13, 1, 1, 1, 1] 231
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 86
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043695 none CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
231  conformations in input
total number of sets (complete confs): 231
using faster count positions algorithm for large data
unique positions, atoms: [77, 41, 77, 77, 13, 41, 13, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 77, 77, 77, 77, 77, 77, 231, 13, 13, 13, 13, 1, 13, 13, 13, 13] 231
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 554
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043695 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043695
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043695/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043695
Building REAL250005043696
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043696'
/scratch/stefan/7916125/working/building/REAL250005043696 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043696

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043696/0 /scratch/stefan/7916125/working/building/REAL250005043696 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/809
`/scratch/stefan/7916125/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043696 none CC1=CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 77, 77, 98, 98, 98, 98, 98, 27, 27, 2, 2, 2, 1, 1, 27, 27, 27, 27, 98, 27, 27, 27, 27] 98
rigid atoms, others: [0, 1, 2, 3, 4, 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])
total number of confs: 228
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043696 none CC1=CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 27, 27, 27, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1] 98
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 113
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: REAL250005043696 none CC1=CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 98, 75, 33, 75, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 98, 98, 98, 98, 98, 33, 33, 33, 33, 1, 33, 33, 33, 33] 98
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 273
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043696 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043696
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043696/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043696
Building REAL250005043697
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043697'
/scratch/stefan/7916125/working/building/REAL250005043697 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043697

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043697/0 /scratch/stefan/7916125/working/building/REAL250005043697 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/810
`/scratch/stefan/7916125/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043697 none CN(C)C(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 25, 31, 7, 25, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 31, 1, 1, 1, 1] 93
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 131
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043697 none CN(C)C(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 66, 93, 27, 64, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 93, 93, 93, 93, 93, 93, 31, 31, 31, 31, 1, 31, 31, 31, 31] 93
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 269
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043697 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043697
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043697/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043697
Building REAL250005043698
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043698'
/scratch/stefan/7916125/working/building/REAL250005043698 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043698

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043698/0 /scratch/stefan/7916125/working/building/REAL250005043698 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/811
`/scratch/stefan/7916125/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043698 none CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [107, 30, 30, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 107, 107, 107, 30, 30, 1, 1, 1, 1, 32, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 219
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043698 none CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 184, 100, 32, 100, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 184, 184, 32, 32, 32, 32, 1, 32, 32, 32, 32] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 553
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043698 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043698
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043698/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043698
Building REAL250005043699
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043699'
/scratch/stefan/7916125/working/building/REAL250005043699 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043699

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043699/0 /scratch/stefan/7916125/working/building/REAL250005043699 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/812
`/scratch/stefan/7916125/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043699 none CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
207  conformations in input
total number of sets (complete confs): 207
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 5, 6, 6, 1, 5, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 10, 10, 10, 10, 10, 6, 6, 6, 18, 1, 1, 1, 1, 25, 1, 1, 1, 1] 207
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 94
number of broken/clashed sets: 161
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043699 none CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
207  conformations in input
total number of sets (complete confs): 207
using faster count positions algorithm for large data
unique positions, atoms: [69, 58, 57, 58, 58, 25, 57, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 69, 69, 69, 69, 69, 58, 58, 58, 174, 25, 25, 25, 25, 1, 25, 25, 25, 25] 207
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 397
number of broken/clashed sets: 161
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043699 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043699
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043699/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043699
Building REAL250005043700
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043700'
/scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005043700

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043700/0 /scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/813
`/scratch/stefan/7916125/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [22, 18, 8, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 22, 22, 22, 22, 22, 18, 18, 18, 8, 8, 1, 1, 1, 1, 21, 1, 1, 1, 1] 87
rigid atoms, others: [32, 33, 34, 35, 37, 6, 39, 8, 9, 10, 11, 12, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 125
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 84, 59, 84, 84, 57, 21, 57, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 87, 87, 87, 87, 87, 84, 84, 84, 59, 59, 21, 21, 21, 21, 1, 21, 21, 21, 21] 87
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 312
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043700/1 /scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/814
`/scratch/stefan/7916125/working/3D/814' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043700.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043700/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [21, 17, 8, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 21, 21, 21, 21, 21, 17, 17, 17, 8, 8, 1, 1, 1, 1, 21, 1, 1, 1, 1] 86
rigid atoms, others: [32, 33, 34, 35, 37, 6, 39, 8, 9, 10, 11, 12, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 122
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 83, 58, 83, 83, 56, 21, 56, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 86, 86, 86, 86, 86, 83, 83, 83, 58, 58, 21, 21, 21, 21, 1, 21, 21, 21, 21] 86
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 310
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `2'
/scratch/stefan/7916125/working/building/REAL250005043700/2 /scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 2 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/815
`/scratch/stefan/7916125/working/3D/815' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043700.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005043700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043700/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 27, 48, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 68, 68, 68, 68, 68, 48, 48, 48, 27, 27, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 319
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043700 none CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 182, 195, 105, 27, 105, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 195, 195, 195, 182, 182, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 728
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043700 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043700
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043700/1.*
2: /scratch/stefan/7916125/working/building/REAL250005043700/2.*
0: /scratch/stefan/7916125/working/building/REAL250005043700/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043700
Building REAL250005043701
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043701'
/scratch/stefan/7916125/working/building/REAL250005043701 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043701

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043701/0 /scratch/stefan/7916125/working/building/REAL250005043701 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/816
`/scratch/stefan/7916125/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1)

`REAL250005043701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043701 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 27, 27, 27, 27, 77, 77, 97, 97, 97, 97, 97, 27, 27, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 97, 27, 27, 27, 27, 1, 1] 97
rigid atoms, others: [0, 1, 2, 3, 4, 35, 20, 21, 22, 23, 24, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 219
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043701 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 31, 1, 1, 1, 1, 27, 27] 97
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 36, 5, 11, 12, 13, 14, 15, 16, 17, 35, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 111
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: REAL250005043701 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 31, 81, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 97, 97, 97, 97, 97, 97, 31, 31, 31, 31, 1, 31, 31, 31, 31, 97, 97] 97
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 265
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043701 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043701
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043701/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043701
Building REAL250005043702
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043702'
/scratch/stefan/7916125/working/building/REAL250005043702 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043702

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043702/0 /scratch/stefan/7916125/working/building/REAL250005043702 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/817
`/scratch/stefan/7916125/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2F)CC1)

`REAL250005043702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043702 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 31, 31, 31, 27, 87, 88, 114, 114, 114, 114, 31, 31, 1, 31, 31, 31, 31, 114, 114, 114, 114, 114, 114, 31, 31, 31, 31] 114
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 317
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043702 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 1, 31, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1] 114
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 109
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: REAL250005043702 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2F)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [88, 26, 88, 114, 114, 114, 114, 114, 26, 26, 26, 8, 1, 8, 1, 1, 1, 1, 1, 26, 26, 114, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 114
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35])
total number of confs: 257
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043702 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043702
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043702/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043702
Building REAL250005043703
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043703'
/scratch/stefan/7916125/working/building/REAL250005043703 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043703

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043703/0 /scratch/stefan/7916125/working/building/REAL250005043703 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/818
`/scratch/stefan/7916125/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CNC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CNC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 99, 99, 119, 119, 119, 119, 119, 34, 34, 1, 1, 1, 34, 34, 34, 34, 119, 34, 34, 34, 34] 119
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 282
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CNC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 34, 34, 34, 34, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 34, 34, 34, 1, 1, 1, 1, 33, 1, 1, 1, 1] 119
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CNC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [91, 33, 91, 119, 119, 119, 119, 33, 33, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 119, 119, 119, 33, 33, 33, 33, 1, 33, 33, 33, 33] 119
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 292
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043703 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043703/1 /scratch/stefan/7916125/working/building/REAL250005043703 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/819
`/scratch/stefan/7916125/working/3D/819' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CN=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043703.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043703/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CN=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 71, 71, 94, 94, 94, 94, 94, 24, 24, 1, 1, 1, 24, 24, 24, 24, 94, 24, 24, 24, 24] 94
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 218
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CN=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 24, 24, 24, 1, 1, 1, 1, 26, 1, 1, 1, 1] 94
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043703 none O=C(C1=CN=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [59, 26, 59, 94, 94, 94, 94, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 94, 94, 94, 26, 26, 26, 26, 1, 26, 26, 26, 26] 94
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 216
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043703 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043703
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043703/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043703/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043703
Building REAL250005043704
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043704'
/scratch/stefan/7916125/working/building/REAL250005043704 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043704

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043704/0 /scratch/stefan/7916125/working/building/REAL250005043704 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/820
`/scratch/stefan/7916125/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1)

`REAL250005043704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043704 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 56, 56, 85, 85, 85, 24, 24, 1, 24, 24, 24, 24, 85, 85, 85, 85, 24, 24, 24, 24] 85
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043704 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 24, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1] 85
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043704 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [56, 15, 56, 85, 85, 85, 85, 85, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 85, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 85
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 193
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043704 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043704
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043704/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043704
Building REAL250005043705
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043705'
/scratch/stefan/7916125/working/building/REAL250005043705 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043705

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043705/0 /scratch/stefan/7916125/working/building/REAL250005043705 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/821
`/scratch/stefan/7916125/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043705 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 102, 102, 131, 131, 131, 131, 131, 33, 33, 1, 1, 1, 1, 1, 33, 33, 33, 33, 131, 33, 33, 33, 33] 131
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043705 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 33, 33, 33, 33, 33, 1, 1, 1, 1, 38, 1, 1, 1, 1] 131
rigid atoms, others: [32, 1, 34, 33, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043705 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [100, 38, 100, 131, 131, 131, 131, 38, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 131, 131, 131, 131, 131, 38, 38, 38, 38, 1, 38, 38, 38, 38] 131
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043705 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043705
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043705/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043705
Building REAL250005043706
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043706'
/scratch/stefan/7916125/working/building/REAL250005043706 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043706

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043706/0 /scratch/stefan/7916125/working/building/REAL250005043706 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/822
`/scratch/stefan/7916125/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043706 none CCC[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [66, 59, 20, 7, 20, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 66, 66, 66, 66, 66, 60, 60, 60, 1, 1, 1, 1, 31, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 385
number of broken/clashed sets: 174
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043706 none CCC[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 146, 94, 146, 146, 31, 94, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 200, 200, 438, 31, 31, 31, 31, 1, 31, 31, 31, 31] 603
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1231
number of broken/clashed sets: 174
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043706 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043706
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043706/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043706
Building REAL250005043707
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043707'
/scratch/stefan/7916125/working/building/REAL250005043707 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043707

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043707/0 /scratch/stefan/7916125/working/building/REAL250005043707 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/823
`/scratch/stefan/7916125/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043707 none CC(C)[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [34, 22, 35, 7, 22, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 35, 35, 35, 35, 35, 35, 35, 66, 1, 1, 1, 1, 27, 1, 1, 1, 1] 372
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 265
number of broken/clashed sets: 130
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043707 none CC(C)[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [124, 113, 124, 81, 113, 113, 27, 81, 27, 27, 27, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 124, 124, 124, 124, 124, 124, 124, 339, 27, 27, 27, 27, 1, 27, 27, 27, 27] 372
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 775
number of broken/clashed sets: 130
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043707 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043707
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043707/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043707
Building REAL250005043708
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043708'
/scratch/stefan/7916125/working/building/REAL250005043708 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043708

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043708/0 /scratch/stefan/7916125/working/building/REAL250005043708 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/824
`/scratch/stefan/7916125/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043708 none CCOC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 73, 27, 27, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 94, 94, 94, 94, 94, 27, 27, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 281
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043708 none CCOC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 147, 147, 71, 17, 71, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 147, 147, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 519
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043708 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043708
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043708/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043708
Building REAL250005043709
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043709'
/scratch/stefan/7916125/working/building/REAL250005043709 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043709

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043709/0 /scratch/stefan/7916125/working/building/REAL250005043709 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/825
`/scratch/stefan/7916125/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043709 none C[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 18, 18, 1, 6, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 18, 18, 18, 54, 1, 1, 1, 1, 27, 1, 1, 1, 1] 210
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 161
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043709 none C[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [70, 60, 70, 70, 27, 60, 27, 27, 27, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 70, 70, 70, 210, 27, 27, 27, 27, 1, 27, 27, 27, 27] 210
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 413
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043709 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043709
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043709/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043709
Building REAL250005043710
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043710'
/scratch/stefan/7916125/working/building/REAL250005043710 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043710

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043710/0 /scratch/stefan/7916125/working/building/REAL250005043710 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/826
`/scratch/stefan/7916125/working/3D/826' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043710 none O=C(CCCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 40, 47, 80, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 24, 24, 43, 43, 47, 47, 80, 80, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 37, 7, 8, 9, 10, 11, 19, 20, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 421
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043710 none O=C(CCCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 77, 131, 177, 201, 201, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 131, 131, 183, 183, 201, 201, 201, 201, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 871
number of broken/clashed sets: 28
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043710 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043710
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043710/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043710
Building REAL250005043711
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043711'
/scratch/stefan/7916125/working/building/REAL250005043711 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043711

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043711/0 /scratch/stefan/7916125/working/building/REAL250005043711 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/827
`/scratch/stefan/7916125/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043711 none O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 98, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 30, 30, 98, 98, 294, 1, 1, 1, 1, 33, 1, 1, 1, 1] 603
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 677
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043711 none O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [108, 33, 108, 181, 181, 201, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 181, 181, 201, 201, 603, 33, 33, 33, 33, 1, 33, 33, 33, 33] 603
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 1232
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043711 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043711
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043711/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043711
Building REAL250005043712
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043712'
/scratch/stefan/7916125/working/building/REAL250005043712 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043712

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043712/0 /scratch/stefan/7916125/working/building/REAL250005043712 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/828
`/scratch/stefan/7916125/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043712 none COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 23, 23, 23, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 35, 1, 1, 1, 1] 145
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 103
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043712 none COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 99, 145, 145, 35, 99, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 145, 145, 145, 145, 145, 145, 145, 145, 145, 35, 35, 35, 35, 1, 35, 35, 35, 35] 145
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 517
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043712 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043712
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043712/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043712
Building REAL250005043713
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043713'
/scratch/stefan/7916125/working/building/REAL250005043713 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043713

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043713/0 /scratch/stefan/7916125/working/building/REAL250005043713 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/829
`/scratch/stefan/7916125/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043713 none O=C(CCCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 30, 38, 70, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 22, 22, 32, 32, 38, 38, 70, 70, 210, 1, 1, 1, 1, 19, 1, 1, 1, 1] 603
rigid atoms, others: [32, 1, 35, 36, 33, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 589
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043713 none O=C(CCCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 73, 127, 165, 201, 201, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 127, 127, 171, 171, 201, 201, 201, 201, 603, 19, 19, 19, 19, 1, 19, 19, 19, 19] 603
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1487
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043713 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043713
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043713/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043713
Building REAL250005043714
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043714'
/scratch/stefan/7916125/working/building/REAL250005043714 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043714

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043714/0 /scratch/stefan/7916125/working/building/REAL250005043714 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/830
`/scratch/stefan/7916125/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CO)CC2)CC1)

`REAL250005043714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043714 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 18, 56, 58, 68, 80, 68, 68, 20, 20, 1, 20, 20, 20, 20, 80, 80, 240, 68, 68, 68, 68, 20, 20, 20, 20] 240
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 493
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043714 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
240  conformations in input
total number of sets (complete confs): 240
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 7, 7, 9, 29, 9, 9, 1, 1, 20, 1, 1, 1, 1, 29, 29, 87, 9, 9, 9, 9, 1, 1, 1, 1] 240
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 221
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: REAL250005043714 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CO)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
237  conformations in input
total number of sets (complete confs): 237
using faster count positions algorithm for large data
unique positions, atoms: [39, 9, 39, 67, 67, 67, 67, 67, 9, 9, 9, 4, 1, 4, 1, 1, 10, 1, 1, 9, 9, 67, 9, 9, 9, 9, 10, 10, 30, 1, 1, 1, 1, 9, 9, 9, 9] 237
rigid atoms, others: [32, 12, 14, 15, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36])
total number of confs: 200
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043714 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043714
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043714/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043714
Building REAL250005043715
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043715'
/scratch/stefan/7916125/working/building/REAL250005043715 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043715

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043715/0 /scratch/stefan/7916125/working/building/REAL250005043715 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/831
`/scratch/stefan/7916125/working/3D/831' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043715 none COC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [56, 24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 56, 56, 56, 24, 1, 1, 1, 1, 35, 1, 1, 1, 1] 167
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 180
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043715 none COC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
167  conformations in input
total number of sets (complete confs): 167
using faster count positions algorithm for large data
unique positions, atoms: [167, 158, 95, 158, 35, 95, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 167, 167, 167, 158, 35, 35, 35, 35, 1, 35, 35, 35, 35] 167
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 585
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043715 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043715
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043715/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043715
Building REAL250005043716
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043716'
/scratch/stefan/7916125/working/building/REAL250005043716 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043716

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043716/0 /scratch/stefan/7916125/working/building/REAL250005043716 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/832
`/scratch/stefan/7916125/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1)

`REAL250005043716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043716 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 54, 54, 67, 67, 67, 67, 25, 25, 1, 25, 25, 25, 25, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 25] 67
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043716 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 1, 1, 25, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 67
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043716 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [51, 13, 51, 67, 67, 67, 67, 67, 13, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 67, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 67
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 148
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043716 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043716
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043716/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043716
Building REAL250005043717
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043717'
/scratch/stefan/7916125/working/building/REAL250005043717 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043717

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043717/0 /scratch/stefan/7916125/working/building/REAL250005043717 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/833
`/scratch/stefan/7916125/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043717 none C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 58, 31, 58, 58, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 79, 79, 79, 58, 58, 58, 31, 31, 1, 1, 1, 1, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 354
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043717 none C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 201, 201, 79, 21, 79, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 201, 158, 158, 21, 21, 21, 21, 1, 21, 21, 21, 21] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 806
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043717 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043717
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043717/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043717
Building REAL250005043718
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043718'
/scratch/stefan/7916125/working/building/REAL250005043718 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043718

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043718/0 /scratch/stefan/7916125/working/building/REAL250005043718 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/834
`/scratch/stefan/7916125/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043718 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 1, 1, 1, 1, 52, 92, 92, 92, 92, 184, 184, 201, 201, 201, 201, 201, 92, 92, 9, 9, 1, 1, 1, 1, 1, 92, 92, 92, 92, 201, 92, 92, 92, 92] 201
rigid atoms, others: [3, 4, 5, 6, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 484
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043718 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 30, 92, 92, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 30, 30, 92, 92, 92, 92, 92, 1, 1, 1, 1, 22, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 276
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: REAL250005043718 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 92, 156, 156, 201, 201, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 156, 156, 201, 201, 201, 201, 201, 22, 22, 22, 22, 1, 22, 22, 22, 22] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 632
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043718 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043718
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043718/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043718
Building REAL250005043719
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043719'
/scratch/stefan/7916125/working/building/REAL250005043719 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043719

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043719/0 /scratch/stefan/7916125/working/building/REAL250005043719 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/835
`/scratch/stefan/7916125/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043719 none CC=C(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 7, 15, 21, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 15, 15, 15, 15, 21, 21, 21, 21, 21, 1, 1, 1, 1, 29, 1, 1, 1, 1] 89
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043719 none CC=C(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 59, 81, 89, 29, 59, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 81, 81, 81, 81, 89, 89, 89, 89, 89, 29, 29, 29, 29, 1, 29, 29, 29, 29] 89
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 284
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043719 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043719
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043719/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043719
Building REAL250005043720
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043720'
/scratch/stefan/7916125/working/building/REAL250005043720 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043720

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043720/0 /scratch/stefan/7916125/working/building/REAL250005043720 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/836
`/scratch/stefan/7916125/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043720 none C=CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [25, 11, 7, 11, 11, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 25, 25, 25, 11, 11, 11, 33, 1, 1, 1, 1, 36, 1, 1, 1, 1] 270
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 160
number of broken/clashed sets: 136
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043720 none C=CC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
270  conformations in input
total number of sets (complete confs): 270
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 88, 90, 90, 31, 88, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 90, 90, 90, 90, 90, 90, 270, 36, 36, 36, 36, 1, 36, 36, 36, 36] 270
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 501
number of broken/clashed sets: 136
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043720 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043720
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043720/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043720
Building REAL250005043721
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043721'
/scratch/stefan/7916125/working/building/REAL250005043721 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043721

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043721/0 /scratch/stefan/7916125/working/building/REAL250005043721 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/837
`/scratch/stefan/7916125/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043721 none O=C(C1=CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 53, 53, 70, 70, 70, 70, 70, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 70, 22, 22, 22, 22] 70
rigid atoms, others: [1, 2, 3, 4, 5, 20, 21, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 157
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043721 none O=C(C1=CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 22, 22, 22, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 22, 22, 22, 22, 22, 1, 1, 1, 1, 37, 1, 1, 1, 1] 70
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 86
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043721 none O=C(C1=CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
70  conformations in input
total number of sets (complete confs): 70
using faster count positions algorithm for large data
unique positions, atoms: [70, 37, 70, 70, 70, 70, 37, 37, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 70, 70, 70, 70, 70, 37, 37, 37, 37, 1, 37, 37, 37, 37] 70
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 174
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043721 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043721
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043721/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043721
Building REAL250005043722
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043722'
/scratch/stefan/7916125/working/building/REAL250005043722 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043722

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043722/0 /scratch/stefan/7916125/working/building/REAL250005043722 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/838
`/scratch/stefan/7916125/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043722 none CON=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [65, 37, 37, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 65, 65, 65, 37, 1, 1, 1, 1, 33, 1, 1, 1, 1] 144
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 181
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043722 none CON=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
144  conformations in input
total number of sets (complete confs): 144
using faster count positions algorithm for large data
unique positions, atoms: [144, 144, 144, 94, 33, 94, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 144, 144, 144, 144, 33, 33, 33, 33, 1, 33, 33, 33, 33] 144
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 419
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043722 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043722
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043722/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043722
Building REAL250005043723
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043723'
/scratch/stefan/7916125/working/building/REAL250005043723 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043723

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043723/0 /scratch/stefan/7916125/working/building/REAL250005043723 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/839
`/scratch/stefan/7916125/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1)

`REAL250005043723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043723 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 32, 32, 32, 64, 64, 83, 83, 83, 32, 32, 1, 32, 32, 32, 32, 83, 83, 83, 83, 32, 32, 32, 32] 83
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043723 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 1, 1, 32, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 1] 83
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043723 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [65, 20, 65, 83, 83, 83, 83, 83, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 20, 20, 83, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 83
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 193
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043723 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043723
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043723/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043723
Building REAL250005043724
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043724'
/scratch/stefan/7916125/working/building/REAL250005043724 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043724

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043724/0 /scratch/stefan/7916125/working/building/REAL250005043724 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/840
`/scratch/stefan/7916125/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043724 none O=C(COCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 44, 78, 98, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 18, 18, 78, 78, 98, 98, 294, 1, 1, 1, 1, 13, 1, 1, 1, 1] 603
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 725
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043724 none O=C(COCCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [47, 13, 47, 97, 177, 201, 201, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 97, 97, 201, 201, 201, 201, 602, 13, 13, 13, 13, 1, 13, 13, 13, 13] 603
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1248
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043724 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043724
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043724/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043724
Building REAL250005043725
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043725'
/scratch/stefan/7916125/working/building/REAL250005043725 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043725

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043725/0 /scratch/stefan/7916125/working/building/REAL250005043725 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/841
`/scratch/stefan/7916125/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043725 none CC(C)(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 6, 1, 3, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 3, 3, 3, 3, 3, 3, 6, 6, 1, 1, 1, 1, 13, 1, 1, 1, 1] 18
rigid atoms, others: [32, 34, 35, 36, 5, 7, 8, 9, 10, 11, 37, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 48
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043725 none CC(C)(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13, 1, 13, 13, 13, 13] 18
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 45
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043725 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043725
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043725/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043725
Building REAL250005043726
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043726'
/scratch/stefan/7916125/working/building/REAL250005043726 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043726

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043726/0 /scratch/stefan/7916125/working/building/REAL250005043726 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/842
`/scratch/stefan/7916125/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOCC2)CC1)

`REAL250005043726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043726 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
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: [10, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 30, 77, 77, 111, 111, 111, 111, 30, 29, 1, 30, 30, 30, 30, 111, 111, 111, 111, 30, 30, 30, 30] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043726 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
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: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 1, 1, 30, 1, 1, 1, 1, 34, 34, 34, 34, 1, 1, 1, 1] 111
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29])
total number of confs: 91
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043726 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
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: [93, 34, 93, 111, 111, 111, 111, 111, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 34, 34, 111, 34, 34, 34, 34, 1, 1, 1, 1, 34, 34, 34, 34] 111
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 260
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043726 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043726
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043726/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043726
Building REAL250005043727
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043727'
/scratch/stefan/7916125/working/building/REAL250005043727 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043727

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043727/0 /scratch/stefan/7916125/working/building/REAL250005043727 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/843
`/scratch/stefan/7916125/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043727 none COCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 58, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 105, 105, 105, 58, 58, 22, 66, 1, 1, 1, 1, 20, 1, 1, 1, 1] 603
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 422
number of broken/clashed sets: 265
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043727 none COCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 147, 76, 147, 20, 76, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 147, 441, 20, 20, 20, 20, 1, 20, 20, 20, 20] 603
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1284
number of broken/clashed sets: 265
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043727 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043727
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043727/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043727
Building REAL250005043728
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043728'
/scratch/stefan/7916125/working/building/REAL250005043728 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043728

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043728/0 /scratch/stefan/7916125/working/building/REAL250005043728 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/844
`/scratch/stefan/7916125/working/3D/844' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043728 none C#CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 5, 6, 6, 1, 5, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 16, 1, 1, 1, 1] 34
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 46
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043728 none C#CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 34, 34, 34, 34, 16, 34, 16, 16, 16, 9, 1, 9, 1, 1, 1, 1, 1, 1, 16, 16, 34, 34, 34, 34, 34, 34, 34, 16, 16, 16, 16, 1, 16, 16, 16, 16] 34
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 88
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043728 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043728
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043728/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043728
Building REAL250005043729
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043729'
/scratch/stefan/7916125/working/building/REAL250005043729 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043729

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043729/0 /scratch/stefan/7916125/working/building/REAL250005043729 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/845
`/scratch/stefan/7916125/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043729 none O=C(COC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 6, 1, 1, 1, 1, 74, 113, 113, 113, 113, 199, 199, 201, 201, 201, 201, 201, 113, 113, 25, 25, 1, 1, 1, 1, 1, 113, 113, 113, 113, 201, 113, 113, 113, 113] 201
rigid atoms, others: [3, 4, 5, 6, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 551
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043729 none O=C(COC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 64, 113, 113, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 21, 21, 113, 113, 113, 113, 113, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 323
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043729 none O=C(COC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 53, 112, 173, 201, 201, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 112, 112, 201, 201, 201, 201, 201, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 633
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043729 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043729
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043729/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043729
Building REAL250005043730
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043730'
/scratch/stefan/7916125/working/building/REAL250005043730 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043730

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043730/0 /scratch/stefan/7916125/working/building/REAL250005043730 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/846
`/scratch/stefan/7916125/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NC=CN2)CC1)

`REAL250005043730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043730 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 59, 59, 59, 59, 59, 59, 25, 25, 1, 25, 25, 25, 25, 59, 59, 59, 25, 25, 25, 25] 59
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 142
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043730 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 1, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 1, 1, 25, 1, 1, 1, 1, 17, 17, 17, 1, 1, 1, 1] 59
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28])
total number of confs: 69
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043730 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NC=CN2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [61, 21, 61, 81, 81, 81, 81, 81, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 21, 21, 81, 21, 21, 21, 21, 1, 1, 1, 21, 21, 21, 21] 81
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32])
total number of confs: 187
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043730 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043730
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043730/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043730
Building REAL250005043731
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043731'
/scratch/stefan/7916125/working/building/REAL250005043731 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043731

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043731/0 /scratch/stefan/7916125/working/building/REAL250005043731 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/847
`/scratch/stefan/7916125/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043731 none CCCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 23, 23, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 90, 90, 90, 90, 90, 64, 64, 23, 23, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 427
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043731 none CCCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 122, 122, 55, 13, 55, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 181, 181, 122, 122, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 807
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043731 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043731
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043731/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043731
Building REAL250005043732
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043732'
/scratch/stefan/7916125/working/building/REAL250005043732 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043732

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043732/0 /scratch/stefan/7916125/working/building/REAL250005043732 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/848
`/scratch/stefan/7916125/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043732 none CC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [31, 31, 7, 31, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 31, 31, 31, 31, 1, 1, 1, 1, 33, 1, 1, 1, 1] 137
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 121
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043732 none CC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
137  conformations in input
total number of sets (complete confs): 137
using faster count positions algorithm for large data
unique positions, atoms: [137, 137, 112, 137, 33, 112, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 137, 137, 137, 137, 33, 33, 33, 33, 1, 33, 33, 33, 33] 137
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 373
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043732 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043732
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043732/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043732
Building REAL250005043733
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043733'
/scratch/stefan/7916125/working/building/REAL250005043733 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043733

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043733/0 /scratch/stefan/7916125/working/building/REAL250005043733 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/849
`/scratch/stefan/7916125/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043733 none CCC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
528  conformations in input
total number of sets (complete confs): 528
using faster count positions algorithm for large data
unique positions, atoms: [21, 16, 7, 16, 57, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 25, 25, 25, 25, 25, 16, 57, 57, 171, 1, 1, 1, 1, 37, 1, 1, 1, 1] 528
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 518
number of broken/clashed sets: 305
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043733 none CCC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
528  conformations in input
total number of sets (complete confs): 528
using faster count positions algorithm for large data
unique positions, atoms: [161, 152, 112, 152, 176, 37, 112, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 176, 176, 176, 176, 176, 152, 176, 176, 528, 37, 37, 37, 37, 1, 37, 37, 37, 37] 528
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1398
number of broken/clashed sets: 305
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043733 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043733
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043733/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043733
Building REAL250005043734
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043734'
/scratch/stefan/7916125/working/building/REAL250005043734 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043734

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043734/0 /scratch/stefan/7916125/working/building/REAL250005043734 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/850
`/scratch/stefan/7916125/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043734 none CC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
390  conformations in input
total number of sets (complete confs): 390
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 17, 51, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 17, 17, 17, 17, 51, 51, 153, 1, 1, 1, 1, 33, 1, 1, 1, 1] 390
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 403
number of broken/clashed sets: 189
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043734 none CC(CO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
390  conformations in input
total number of sets (complete confs): 390
using faster count positions algorithm for large data
unique positions, atoms: [129, 108, 129, 130, 33, 108, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 129, 129, 129, 129, 130, 130, 390, 33, 33, 33, 33, 1, 33, 33, 33, 33] 390
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 783
number of broken/clashed sets: 189
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043734 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043734
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043734/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043734
Building REAL250005043735
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043735'
/scratch/stefan/7916125/working/building/REAL250005043735 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043735

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043735/0 /scratch/stefan/7916125/working/building/REAL250005043735 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/851
`/scratch/stefan/7916125/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CON=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043735 none O=C(C1=CON=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 11, 29, 29, 29, 29, 77, 77, 107, 107, 107, 107, 107, 29, 29, 1, 1, 29, 29, 29, 29, 107, 29, 29, 29, 29] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 235
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043735 none O=C(C1=CON=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 29, 29, 29, 29, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 29, 29, 1, 1, 1, 1, 29, 1, 1, 1, 1] 107
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 85
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043735 none O=C(C1=CON=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [55, 29, 55, 107, 107, 107, 107, 29, 29, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 107, 107, 29, 29, 29, 29, 1, 29, 29, 29, 29] 107
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 238
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043735 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043735
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043735/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043735
Building REAL250005043736
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043736'
/scratch/stefan/7916125/working/building/REAL250005043736 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043736

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043736/0 /scratch/stefan/7916125/working/building/REAL250005043736 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/852
`/scratch/stefan/7916125/working/3D/852' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2C[C@H]2CF)CC1)

`REAL250005043736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043736 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2C[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 32, 101, 101, 182, 182, 182, 182, 182, 201, 32, 30, 1, 32, 32, 32, 32, 182, 182, 201, 201, 32, 32, 32, 32] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 638
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043736 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2C[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 27, 101, 1, 1, 32, 1, 1, 1, 1, 27, 27, 101, 101, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 28, 29, 30, 31])
total number of confs: 400
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: REAL250005043736 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2C[C@H]2CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [109, 27, 109, 182, 182, 182, 182, 182, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 9, 27, 27, 182, 27, 27, 27, 27, 1, 1, 9, 9, 27, 27, 27, 27] 201
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35])
total number of confs: 401
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043736 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043736
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043736/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043736
Building REAL250005043737
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043737'
/scratch/stefan/7916125/working/building/REAL250005043737 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043737

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043737/0 /scratch/stefan/7916125/working/building/REAL250005043737 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/853
`/scratch/stefan/7916125/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043737 none C#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 55, 55, 79, 79, 79, 79, 79, 11, 11, 1, 1, 1, 11, 11, 11, 11, 79, 11, 11, 11, 11, 1, 1, 1, 1] 79
rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 19, 20, 21, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30])
total number of confs: 173
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043737 none C#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 11, 11, 11, 1, 1, 1, 1, 32, 1, 1, 1, 1, 11, 11, 11, 11] 79
rigid atoms, others: [3, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30] set([0, 1, 2, 34, 4, 33, 32, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 26, 31])
total number of confs: 76
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043737 none C#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
79  conformations in input
total number of sets (complete confs): 79
using faster count positions algorithm for large data
unique positions, atoms: [79, 79, 76, 32, 76, 32, 32, 32, 11, 1, 11, 1, 1, 1, 1, 1, 1, 32, 32, 79, 79, 79, 32, 32, 32, 32, 1, 32, 32, 32, 32, 79, 79, 79, 79] 79
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 196
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043737 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043737
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043737/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043737
Building REAL250005043738
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043738'
/scratch/stefan/7916125/working/building/REAL250005043738 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043738

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043738/0 /scratch/stefan/7916125/working/building/REAL250005043738 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/854
`/scratch/stefan/7916125/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=COCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043738 none O=C(C1=COCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 90, 90, 118, 118, 118, 118, 118, 27, 27, 1, 1, 1, 1, 1, 27, 27, 27, 27, 118, 27, 27, 27, 27] 118
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 271
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043738 none O=C(C1=COCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 27, 27, 27, 27, 27, 1, 1, 1, 1, 36, 1, 1, 1, 1] 118
rigid atoms, others: [32, 1, 34, 33, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 90
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: REAL250005043738 none O=C(C1=COCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [80, 36, 80, 118, 118, 118, 118, 36, 36, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 36, 36, 118, 118, 118, 118, 118, 36, 36, 36, 36, 1, 36, 36, 36, 36] 118
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 269
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043738 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043738
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043738/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043738
Building REAL250005043739
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043739'
/scratch/stefan/7916125/working/building/REAL250005043739 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043739

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043739/0 /scratch/stefan/7916125/working/building/REAL250005043739 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/855
`/scratch/stefan/7916125/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043739 none C[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [18, 6, 18, 18, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 18, 18, 18, 54, 1, 1, 1, 1, 25, 1, 1, 1, 1] 210
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 159
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043739 none C[C@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [70, 59, 70, 70, 25, 59, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 70, 70, 70, 210, 25, 25, 25, 25, 1, 25, 25, 25, 25] 210
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 419
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043739 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043739
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043739/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043739
Building REAL250005043740
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043740'
/scratch/stefan/7916125/working/building/REAL250005043740 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043740

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043740/0 /scratch/stefan/7916125/working/building/REAL250005043740 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/856
`/scratch/stefan/7916125/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C=CCC2)CC1)

`REAL250005043740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043740 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 31, 31, 31, 28, 71, 72, 91, 91, 91, 91, 31, 31, 1, 31, 31, 31, 31, 91, 91, 91, 91, 91, 91, 91, 31, 31, 31, 31] 91
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 253
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043740 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 1, 1, 31, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 91
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 93
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: REAL250005043740 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C=CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [68, 18, 68, 91, 91, 91, 91, 91, 18, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 18, 18, 91, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 91
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 201
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043740 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043740
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043740/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043740
Building REAL250005043741
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043741'
/scratch/stefan/7916125/working/building/REAL250005043741 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043741

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043741/0 /scratch/stefan/7916125/working/building/REAL250005043741 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/857
`/scratch/stefan/7916125/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043741 none CC(O)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
315  conformations in input
total number of sets (complete confs): 315
using faster count positions algorithm for large data
unique positions, atoms: [26, 15, 28, 7, 15, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 28, 28, 28, 28, 84, 15, 15, 15, 15, 1, 1, 1, 1, 29, 1, 1, 1, 1] 315
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 261
number of broken/clashed sets: 180
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043741 none CC(O)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
315  conformations in input
total number of sets (complete confs): 315
using faster count positions algorithm for large data
unique positions, atoms: [104, 97, 105, 76, 97, 29, 76, 29, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 105, 105, 105, 105, 315, 97, 97, 97, 97, 29, 29, 29, 29, 1, 29, 29, 29, 29] 315
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 675
number of broken/clashed sets: 180
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043741 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043741
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043741/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043741
Building REAL250005043742
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043742'
/scratch/stefan/7916125/working/building/REAL250005043742 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043742

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043742/0 /scratch/stefan/7916125/working/building/REAL250005043742 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/858
`/scratch/stefan/7916125/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043742 none C=C1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 23, 23, 23, 23, 71, 71, 92, 92, 92, 92, 92, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23, 92, 23, 23, 23, 23] 92
rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 209
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043742 none C=C1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1, 33, 1, 1, 1, 1] 92
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 105
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: REAL250005043742 none C=C1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 75, 33, 75, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 92, 92, 92, 92, 92, 33, 33, 33, 33, 1, 33, 33, 33, 33] 92
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 245
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043742 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043742
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043742/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043742
Building REAL250005043743
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043743'
/scratch/stefan/7916125/working/building/REAL250005043743 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043743

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043743/0 /scratch/stefan/7916125/working/building/REAL250005043743 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/859
`/scratch/stefan/7916125/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043743 none CC(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 17, 55, 1, 7, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 17, 17, 17, 17, 55, 55, 1, 1, 1, 1, 23, 1, 1, 1, 1] 118
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 252
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043743 none CC(CF)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
118  conformations in input
total number of sets (complete confs): 118
using faster count positions algorithm for large data
unique positions, atoms: [102, 74, 102, 118, 23, 74, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 102, 102, 102, 102, 118, 118, 23, 23, 23, 23, 1, 23, 23, 23, 23] 118
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 432
number of broken/clashed sets: 54
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043743 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043743
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043743/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043743
Building REAL250005043744
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043744'
/scratch/stefan/7916125/working/building/REAL250005043744 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043744

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043744/0 /scratch/stefan/7916125/working/building/REAL250005043744 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/860
`/scratch/stefan/7916125/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043744 none C=C(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [70, 33, 70, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 70, 70, 70, 70, 70, 33, 33, 1, 1, 1, 1, 35, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 274
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043744 none C=C(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 119, 35, 119, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 201, 201, 201, 201, 201, 200, 200, 35, 35, 35, 35, 1, 35, 35, 35, 35] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 705
number of broken/clashed sets: 49
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043744 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043744
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043744/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043744
Building REAL250005043745
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043745'
/scratch/stefan/7916125/working/building/REAL250005043745 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043745

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043745/0 /scratch/stefan/7916125/working/building/REAL250005043745 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/861
`/scratch/stefan/7916125/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043745 none CCSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 88, 88, 88, 87, 87, 24, 24, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 315
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043745 none CCSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 135, 59, 13, 59, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 135, 135, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 676
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043745 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043745
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043745/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043745
Building REAL250005043746
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043746'
/scratch/stefan/7916125/working/building/REAL250005043746 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043746

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043746/0 /scratch/stefan/7916125/working/building/REAL250005043746 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/862
`/scratch/stefan/7916125/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043746 none CC(C)=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 33, 1, 1, 1, 1] 73
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 93
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043746 none CC(C)=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
73  conformations in input
total number of sets (complete confs): 73
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 53, 73, 33, 53, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 73, 73, 73, 73, 73, 73, 73, 73, 73, 33, 33, 33, 33, 1, 33, 33, 33, 33] 73
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 207
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043746 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043746
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043746/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043746
Building REAL250005043747
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043747'
/scratch/stefan/7916125/working/building/REAL250005043747 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043747

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043747/0 /scratch/stefan/7916125/working/building/REAL250005043747 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/863
`/scratch/stefan/7916125/working/3D/863' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043747 none CCCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [65, 60, 21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 65, 65, 65, 65, 65, 60, 60, 21, 63, 1, 1, 1, 1, 31, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 372
number of broken/clashed sets: 183
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043747 none CCCC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 200, 148, 96, 148, 31, 96, 31, 31, 31, 10, 1, 10, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 201, 200, 200, 148, 444, 31, 31, 31, 31, 1, 31, 31, 31, 31] 603
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1233
number of broken/clashed sets: 183
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043747 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043747
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043747/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043747
Building REAL250005043748
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043748'
/scratch/stefan/7916125/working/building/REAL250005043748 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043748

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043748/0 /scratch/stefan/7916125/working/building/REAL250005043748 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/864
`/scratch/stefan/7916125/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043748 none CCC(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [53, 42, 22, 42, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 53, 53, 53, 53, 53, 42, 126, 22, 22, 1, 1, 1, 1, 28, 1, 1, 1, 1] 531
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 393
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043748 none CCC(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 172, 136, 172, 100, 28, 100, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 177, 177, 177, 177, 177, 172, 516, 136, 136, 28, 28, 28, 28, 1, 28, 28, 28, 28] 531
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1191
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043748 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043748
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043748/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043748
Building REAL250005043749
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043749'
/scratch/stefan/7916125/working/building/REAL250005043749 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043749

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043749/0 /scratch/stefan/7916125/working/building/REAL250005043749 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/865
`/scratch/stefan/7916125/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(Cl)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043749 none CC(Cl)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [29, 29, 29, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 29, 29, 29, 29, 1, 1, 1, 1, 37, 1, 1, 1, 1] 111
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 121
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043749 none CC(Cl)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 79, 37, 79, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 111, 111, 111, 111, 37, 37, 37, 37, 1, 37, 37, 37, 37] 111
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 311
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043749 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043749
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043749/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043749
Building REAL250005043750
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043750'
/scratch/stefan/7916125/working/building/REAL250005043750 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043750

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043750/0 /scratch/stefan/7916125/working/building/REAL250005043750 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/866
`/scratch/stefan/7916125/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043750 none CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 26, 26, 26, 26, 26, 1, 1, 1, 1, 35, 1, 1, 1, 1] 91
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 113
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043750 none CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [91, 91, 79, 35, 79, 35, 35, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 35, 35, 91, 91, 91, 91, 91, 35, 35, 35, 35, 1, 35, 35, 35, 35] 91
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 235
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043750 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043750
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043750/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043750
Building REAL250005043751
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043751'
/scratch/stefan/7916125/working/building/REAL250005043751 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043751

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043751/0 /scratch/stefan/7916125/working/building/REAL250005043751 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/867
`/scratch/stefan/7916125/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1F)

`REAL250005043751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043751 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 4, 8, 8, 8, 8, 31, 31, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 45, 8, 8, 8, 8, 1, 1, 1] 45
rigid atoms, others: [0, 1, 2, 35, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 104
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043751 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [8, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 8, 8] 45
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 34, 3, 35, 33, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 28])
total number of confs: 48
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043751 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 39, 16, 39, 16, 16, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 45, 45, 45, 45, 45, 45, 16, 16, 16, 16, 1, 16, 16, 16, 16, 45, 45, 45] 45
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 126
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043751 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043751
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043751/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043751
Building REAL250005043752
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043752'
/scratch/stefan/7916125/working/building/REAL250005043752 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043752

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043752/0 /scratch/stefan/7916125/working/building/REAL250005043752 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/868
`/scratch/stefan/7916125/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2C[C@@H](O)C2)CC1)

`REAL250005043752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043752 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2C[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
339  conformations in input
total number of sets (complete confs): 339
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 35, 89, 89, 113, 113, 113, 113, 113, 113, 35, 35, 1, 35, 35, 35, 35, 113, 113, 339, 113, 113, 35, 35, 35, 35] 339
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 648
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043752 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2C[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
339  conformations in input
total number of sets (complete confs): 339
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 1, 1, 35, 1, 1, 1, 1, 25, 25, 75, 25, 25, 1, 1, 1, 1] 339
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 21, 22, 24, 25, 26, 27] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 28, 29, 30, 31])
total number of confs: 186
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: REAL250005043752 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2C[C@@H](O)C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
339  conformations in input
total number of sets (complete confs): 339
using faster count positions algorithm for large data
unique positions, atoms: [88, 25, 88, 113, 113, 113, 113, 113, 25, 25, 25, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25, 113, 25, 25, 25, 25, 1, 1, 6, 1, 1, 25, 25, 25, 25] 339
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 30, 33, 34, 35, 36])
total number of confs: 265
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043752 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043752
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043752/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043752
Building REAL250005043753
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043753'
/scratch/stefan/7916125/working/building/REAL250005043753 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043753

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043753/0 /scratch/stefan/7916125/working/building/REAL250005043753 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/869
`/scratch/stefan/7916125/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043753 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 78, 78, 96, 96, 96, 96, 96, 24, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 96, 24, 24, 24, 24] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043753 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 31])
total number of confs: 105
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: REAL250005043753 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 73, 96, 31, 73, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 96, 96, 96, 96, 96, 31, 31, 31, 31, 1, 31, 31, 31, 31] 96
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 271
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043753 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043753
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043753/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043753
Building REAL250005043754
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043754'
/scratch/stefan/7916125/working/building/REAL250005043754 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043754

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043754/0 /scratch/stefan/7916125/working/building/REAL250005043754 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/870
`/scratch/stefan/7916125/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043754 none CNC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 91, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 91, 91, 91, 91, 27, 27, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 304
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043754 none CNC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 201, 70, 15, 70, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201, 161, 161, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 726
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043754 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043754
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043754/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043754
Building REAL250005043755
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043755'
/scratch/stefan/7916125/working/building/REAL250005043755 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043755

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043755/0 /scratch/stefan/7916125/working/building/REAL250005043755 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/871
`/scratch/stefan/7916125/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043755 none C=CC=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 93, 93, 93, 93, 93, 29, 29, 1, 1, 1, 1, 16, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 307
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043755 none C=CC=CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 142, 64, 16, 64, 16, 16, 16, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 16, 201, 201, 201, 201, 201, 142, 142, 16, 16, 16, 16, 1, 16, 16, 16, 16] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 754
number of broken/clashed sets: 45
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043755 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043755
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043755/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043755
Building REAL250005043756
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043756'
/scratch/stefan/7916125/working/building/REAL250005043756 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043756

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043756/0 /scratch/stefan/7916125/working/building/REAL250005043756 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/872
`/scratch/stefan/7916125/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043756 none NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 87, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 88, 88, 32, 32, 24, 24, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 319
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043756 none NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 135, 83, 19, 83, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 171, 171, 135, 135, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 788
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043756 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043756
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043756/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043756
Building REAL250005043757
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043757'
/scratch/stefan/7916125/working/building/REAL250005043757 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043757

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043757/0 /scratch/stefan/7916125/working/building/REAL250005043757 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/873
`/scratch/stefan/7916125/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043757 none CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 70, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 70, 70, 70, 70, 210, 33, 33, 22, 22, 1, 1, 1, 1, 22, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 554
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043757 none CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 162, 201, 145, 90, 22, 90, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 603, 163, 163, 145, 145, 22, 22, 22, 22, 1, 22, 22, 22, 22] 603
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1406
number of broken/clashed sets: 115
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043757 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043757
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043757/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043757
Building REAL250005043758
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043758'
/scratch/stefan/7916125/working/building/REAL250005043758 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043758

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043758/0 /scratch/stefan/7916125/working/building/REAL250005043758 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/874
`/scratch/stefan/7916125/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043758 none C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 52, 52, 52, 20, 20, 20, 20, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 265
number of broken/clashed sets: 102
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043758 none C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 112, 158, 36, 112, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 158, 158, 158, 158, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 782
number of broken/clashed sets: 102
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043758 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043758
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043758/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043758
Building REAL250005043759
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043759'
/scratch/stefan/7916125/working/building/REAL250005043759 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043759

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043759/0 /scratch/stefan/7916125/working/building/REAL250005043759 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/875
`/scratch/stefan/7916125/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043759 none CC(CCO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 42, 67, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 18, 18, 18, 18, 44, 44, 67, 65, 201, 1, 1, 1, 1, 35, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 566
number of broken/clashed sets: 344
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043759 none CC(CCO)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [166, 113, 166, 198, 201, 35, 113, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 166, 166, 166, 166, 201, 201, 201, 198, 603, 35, 35, 35, 35, 1, 35, 35, 35, 35] 603
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1375
number of broken/clashed sets: 344
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043759 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043759
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043759/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043759
Building REAL250005043760
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043760'
/scratch/stefan/7916125/working/building/REAL250005043760 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043760

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043760/0 /scratch/stefan/7916125/working/building/REAL250005043760 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/876
`/scratch/stefan/7916125/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H](O)CF)CC1)

`REAL250005043760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043760 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H](O)CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
1  hydrogens need rotated
315  conformations in input
total number of sets (complete confs): 315
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 64, 64, 97, 97, 97, 105, 17, 17, 1, 17, 17, 17, 17, 291, 105, 105, 17, 17, 17, 17] 315
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 668
number of broken/clashed sets: 133
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043760 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H](O)CF)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
1  hydrogens need rotated
315  conformations in input
total number of sets (complete confs): 315
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 49, 1, 1, 17, 1, 1, 1, 1, 60, 49, 49, 1, 1, 1, 1] 315
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28])
total number of confs: 292
number of broken/clashed sets: 133
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043760 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043760
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043760/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043760
Building REAL250005043761
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043761'
/scratch/stefan/7916125/working/building/REAL250005043761 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043761

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043761/0 /scratch/stefan/7916125/working/building/REAL250005043761 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/877
`/scratch/stefan/7916125/working/3D/877' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CC2)CC1)

`REAL250005043761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043761 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 59, 59, 78, 78, 78, 30, 30, 1, 30, 30, 30, 30, 234, 78, 78, 78, 78, 30, 30, 30, 30] 234
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 455
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043761 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 1, 1, 30, 1, 1, 1, 1, 54, 18, 18, 18, 18, 1, 1, 1, 1] 234
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 146
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: REAL250005043761 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(O)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
234  conformations in input
total number of sets (complete confs): 234
using faster count positions algorithm for large data
unique positions, atoms: [58, 18, 58, 78, 78, 78, 78, 78, 18, 18, 18, 9, 1, 9, 1, 1, 1, 1, 18, 18, 78, 18, 18, 18, 18, 6, 1, 1, 1, 1, 18, 18, 18, 18] 234
rigid atoms, others: [12, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33])
total number of confs: 188
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043761 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043761
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043761/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043761
Building REAL250005043762
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043762'
/scratch/stefan/7916125/working/building/REAL250005043762 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043762

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043762/0 /scratch/stefan/7916125/working/building/REAL250005043762 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/878
`/scratch/stefan/7916125/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043762 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [19, 3, 1, 1, 1, 1, 19, 41, 41, 41, 41, 137, 137, 171, 171, 171, 171, 171, 41, 41, 3, 3, 1, 1, 1, 1, 1, 41, 41, 41, 41, 171, 41, 41, 41, 41] 171
rigid atoms, others: [2, 3, 4, 5, 22, 23, 24, 25, 26] set([0, 1, 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])
total number of confs: 404
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043762 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 26, 41, 41, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 26, 26, 41, 41, 41, 41, 41, 1, 1, 1, 1, 35, 1, 1, 1, 1] 171
rigid atoms, others: [32, 1, 34, 35, 33, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 197
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: REAL250005043762 none O=C(CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
171  conformations in input
total number of sets (complete confs): 171
using faster count positions algorithm for large data
unique positions, atoms: [97, 35, 97, 141, 171, 171, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 141, 141, 171, 171, 171, 171, 171, 35, 35, 35, 35, 1, 35, 35, 35, 35] 171
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 581
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043762 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043762
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043762/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043762
Building REAL250005043763
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043763'
/scratch/stefan/7916125/working/building/REAL250005043763 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043763

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043763/0 /scratch/stefan/7916125/working/building/REAL250005043763 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/879
`/scratch/stefan/7916125/working/3D/879' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043763 none CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 11, 11, 1, 5, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 23, 1, 1, 1, 1] 81
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 77
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043763 none CC(C)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 54, 81, 81, 23, 54, 23, 23, 23, 11, 1, 11, 1, 1, 1, 1, 1, 1, 23, 23, 81, 81, 81, 81, 81, 81, 23, 23, 23, 23, 1, 23, 23, 23, 23] 81
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 296
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043763 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043763
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043763/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043763
Building REAL250005043764
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043764'
/scratch/stefan/7916125/working/building/REAL250005043764 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043764

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043764/0 /scratch/stefan/7916125/working/building/REAL250005043764 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/880
`/scratch/stefan/7916125/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043764 none CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [17, 7, 17, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 17, 17, 17, 1, 1, 1, 1, 29, 1, 1, 1, 1] 68
rigid atoms, others: [4, 6, 7, 8, 9, 10, 18, 19, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 27])
total number of confs: 99
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043764 none CC(F)(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
68  conformations in input
total number of sets (complete confs): 68
using faster count positions algorithm for large data
unique positions, atoms: [68, 59, 68, 68, 29, 59, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 68, 68, 68, 29, 29, 29, 29, 1, 29, 29, 29, 29] 68
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 183
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043764 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043764
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043764/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043764
Building REAL250005043765
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043765'
/scratch/stefan/7916125/working/building/REAL250005043765 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043765

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043765/0 /scratch/stefan/7916125/working/building/REAL250005043765 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/881
`/scratch/stefan/7916125/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043765 none COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [64, 28, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 65, 65, 65, 28, 28, 1, 1, 1, 1, 37, 1, 1, 1, 1] 175
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 207
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043765 none COCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [175, 165, 101, 37, 101, 37, 37, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 175, 175, 175, 165, 165, 37, 37, 37, 37, 1, 37, 37, 37, 37] 175
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 588
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043765 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043765
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043765/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043765
Building REAL250005043766
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043766'
/scratch/stefan/7916125/working/building/REAL250005043766 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043766

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043766/0 /scratch/stefan/7916125/working/building/REAL250005043766 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/882
`/scratch/stefan/7916125/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043766 none CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [41, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 44, 44, 44, 43, 43, 27, 27, 1, 1, 1, 1, 29, 1, 1, 1, 1] 149
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 248
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043766 none CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
149  conformations in input
total number of sets (complete confs): 149
using faster count positions algorithm for large data
unique positions, atoms: [149, 145, 88, 29, 88, 29, 29, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 149, 149, 149, 149, 149, 145, 145, 29, 29, 29, 29, 1, 29, 29, 29, 29] 149
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 550
number of broken/clashed sets: 39
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043766 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043766
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043766/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043766
Building REAL250005043767
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043767'
/scratch/stefan/7916125/working/building/REAL250005043767 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043767

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043767/0 /scratch/stefan/7916125/working/building/REAL250005043767 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/883
`/scratch/stefan/7916125/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043767 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 98, 98, 116, 116, 116, 116, 116, 33, 33, 1, 1, 1, 33, 33, 33, 33, 116, 33, 33, 33, 33] 116
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 281
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043767 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 33, 33, 33, 1, 1, 1, 1, 33, 1, 1, 1, 1] 116
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043767 none O=C(C1=CC=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [86, 33, 86, 116, 116, 116, 116, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 116, 116, 116, 33, 33, 33, 33, 1, 33, 33, 33, 33] 116
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 269
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043767 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043767
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043767/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043767
Building REAL250005043768
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043768'
/scratch/stefan/7916125/working/building/REAL250005043768 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043768

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043768/0 /scratch/stefan/7916125/working/building/REAL250005043768 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/884
`/scratch/stefan/7916125/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043768 none CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [59, 58, 59, 25, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 59, 59, 59, 58, 25, 25, 1, 1, 1, 1, 29, 1, 1, 1, 1] 138
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 224
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043768 none CC(=O)NCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
138  conformations in input
total number of sets (complete confs): 138
using faster count positions algorithm for large data
unique positions, atoms: [138, 138, 138, 115, 88, 29, 88, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 138, 138, 138, 138, 115, 115, 29, 29, 29, 29, 1, 29, 29, 29, 29] 138
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 435
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043768 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043768
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043768/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043768
Building REAL250005043769
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043769'
/scratch/stefan/7916125/working/building/REAL250005043769 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043769

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043769/0 /scratch/stefan/7916125/working/building/REAL250005043769 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/885
`/scratch/stefan/7916125/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043769 none CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [28, 23, 32, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 32, 32, 32, 32, 32, 32, 32, 23, 23, 1, 1, 1, 1, 32, 1, 1, 1, 1] 120
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 205
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043769 none CC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [117, 116, 120, 83, 32, 83, 32, 32, 32, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 32, 120, 120, 120, 120, 120, 120, 120, 116, 116, 32, 32, 32, 32, 1, 32, 32, 32, 32] 120
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 401
number of broken/clashed sets: 52
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043769 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043769
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043769/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043769
Building REAL250005043770
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043770'
/scratch/stefan/7916125/working/building/REAL250005043770 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043770

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043770/0 /scratch/stefan/7916125/working/building/REAL250005043770 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/886
`/scratch/stefan/7916125/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043770 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 60, 60, 72, 72, 72, 72, 72, 21, 21, 2, 2, 2, 1, 1, 1, 1, 21, 21, 21, 21, 72, 21, 21, 21, 21] 72
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26] set([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])
total number of confs: 170
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043770 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 28, 1, 1, 1, 1] 72
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 96
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: REAL250005043770 none CC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 62, 28, 62, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 72, 72, 72, 72, 72, 72, 72, 28, 28, 28, 28, 1, 28, 28, 28, 28] 72
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 185
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043770 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043770
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043770/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043770
Building REAL250005043771
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043771'
/scratch/stefan/7916125/working/building/REAL250005043771 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043771

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043771/0 /scratch/stefan/7916125/working/building/REAL250005043771 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/887
`/scratch/stefan/7916125/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043771 none CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 77, 77, 77, 76, 76, 24, 24, 1, 1, 1, 1, 23, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 236
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043771 none CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 85, 23, 85, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 159, 159, 23, 23, 23, 23, 1, 23, 23, 23, 23] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 652
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043771 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043771
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043771/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043771
Building REAL250005043772
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043772'
/scratch/stefan/7916125/working/building/REAL250005043772 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043772

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043772/0 /scratch/stefan/7916125/working/building/REAL250005043772 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/888
`/scratch/stefan/7916125/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043772 none CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 31, 1, 1, 1, 1] 95
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 107
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043772 none CC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
95  conformations in input
total number of sets (complete confs): 95
using faster count positions algorithm for large data
unique positions, atoms: [95, 95, 95, 73, 31, 71, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 95, 95, 95, 95, 95, 95, 95, 31, 31, 31, 31, 1, 31, 31, 31, 31] 95
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 275
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043772 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043772
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043772/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043772
Building REAL250005043773
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043773'
/scratch/stefan/7916125/working/building/REAL250005043773 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043773

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043773/0 /scratch/stefan/7916125/working/building/REAL250005043773 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/889
`/scratch/stefan/7916125/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1)

`REAL250005043773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043773 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 80, 80, 98, 98, 98, 98, 28, 28, 1, 28, 28, 28, 28, 98, 98, 98, 98, 98, 98, 98, 28, 28, 28, 28] 98
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 258
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043773 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 1, 1, 28, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 98
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 98
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: REAL250005043773 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [82, 23, 82, 98, 98, 98, 98, 98, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 23, 23, 98, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 98
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 224
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043773 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043773
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043773/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043773
Building REAL250005043774
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043774'
/scratch/stefan/7916125/working/building/REAL250005043774 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043774

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043774/0 /scratch/stefan/7916125/working/building/REAL250005043774 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/890
`/scratch/stefan/7916125/working/3D/890' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043774 none CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 26, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 87, 87, 87, 26, 26, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 211
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043774 none CSCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 149, 73, 19, 73, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 149, 149, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 651
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043774 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043774
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043774/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043774
Building REAL250005043775
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043775'
/scratch/stefan/7916125/working/building/REAL250005043775 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043775

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043775/0 /scratch/stefan/7916125/working/building/REAL250005043775 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/891
`/scratch/stefan/7916125/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043775 none CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 63, 63, 63, 20, 20, 18, 18, 1, 1, 1, 1, 33, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 183
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043775 none CSCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 117, 93, 33, 93, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 32, 33, 201, 201, 201, 119, 119, 117, 117, 33, 33, 33, 33, 1, 33, 33, 33, 33] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 500
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043775 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043775
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043775/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043775
Building REAL250005043776
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043776'
/scratch/stefan/7916125/working/building/REAL250005043776 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043776

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043776/0 /scratch/stefan/7916125/working/building/REAL250005043776 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/892
`/scratch/stefan/7916125/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043776 none CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 27, 34, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 34, 34, 34, 34, 34, 34, 34, 27, 27, 19, 19, 1, 1, 1, 1, 28, 1, 1, 1, 1] 133
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 195
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043776 none CC(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 129, 133, 116, 81, 28, 81, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 133, 133, 133, 133, 133, 133, 133, 129, 129, 116, 116, 28, 28, 28, 28, 1, 28, 28, 28, 28] 133
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043776 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043776
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043776/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043776
Building REAL250005043777
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043777'
/scratch/stefan/7916125/working/building/REAL250005043777 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043777

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043777/0 /scratch/stefan/7916125/working/building/REAL250005043777 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/893
`/scratch/stefan/7916125/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043777 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 77, 77, 107, 107, 107, 107, 107, 27, 27, 1, 1, 1, 1, 27, 27, 27, 27, 107, 27, 27, 27, 27] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 238
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043777 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 27, 27, 27, 27, 1, 1, 1, 1, 29, 1, 1, 1, 1] 107
rigid atoms, others: [32, 1, 33, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 83
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043777 none O=C(C1=CC=CN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [66, 29, 66, 107, 107, 107, 107, 29, 29, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 29, 29, 107, 107, 107, 107, 29, 29, 29, 29, 1, 29, 29, 29, 29] 107
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 241
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043777 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043777
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043777/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043777
Building REAL250005043778
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043778'
/scratch/stefan/7916125/working/building/REAL250005043778 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043778

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043778/0 /scratch/stefan/7916125/working/building/REAL250005043778 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/894
`/scratch/stefan/7916125/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043778 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 11, 27, 27, 27, 27, 79, 79, 106, 106, 106, 106, 106, 27, 27, 1, 1, 1, 27, 27, 27, 27, 106, 27, 27, 27, 27] 106
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 241
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043778 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 27, 27, 27, 27, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 27, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1] 106
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 87
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043778 none O=C(C1=COC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
106  conformations in input
total number of sets (complete confs): 106
using faster count positions algorithm for large data
unique positions, atoms: [73, 33, 73, 106, 106, 106, 106, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 106, 106, 106, 33, 33, 33, 33, 1, 33, 33, 33, 33] 106
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 241
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043778 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043778
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043778/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043778
Building REAL250005043779
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043779'
/scratch/stefan/7916125/working/building/REAL250005043779 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043779

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043779/0 /scratch/stefan/7916125/working/building/REAL250005043779 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/895
`/scratch/stefan/7916125/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043779 none CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 42, 28, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 50, 50, 50, 50, 50, 42, 42, 30, 30, 18, 18, 1, 1, 1, 1, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 293
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043779 none CCCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 140, 83, 21, 83, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 201, 201, 162, 162, 140, 140, 21, 21, 21, 21, 1, 21, 21, 21, 21] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 829
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043779 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043779
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043779/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043779
Building REAL250005043780
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043780'
/scratch/stefan/7916125/working/building/REAL250005043780 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043780

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043780/0 /scratch/stefan/7916125/working/building/REAL250005043780 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/896
`/scratch/stefan/7916125/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043780 none CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [24, 17, 24, 24, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 17, 17, 1, 1, 1, 1, 28, 1, 1, 1, 1] 121
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 143
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043780 none CC(C)(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
121  conformations in input
total number of sets (complete confs): 121
using faster count positions algorithm for large data
unique positions, atoms: [121, 117, 121, 121, 82, 28, 82, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 121, 121, 121, 121, 121, 121, 121, 121, 121, 117, 117, 28, 28, 28, 28, 1, 28, 28, 28, 28] 121
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 414
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043780 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043780
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043780/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043780
Building REAL250005043781
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043781'
/scratch/stefan/7916125/working/building/REAL250005043781 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043781

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043781/0 /scratch/stefan/7916125/working/building/REAL250005043781 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/897
`/scratch/stefan/7916125/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043781 none CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [46, 31, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 47, 47, 47, 46, 46, 35, 35, 19, 19, 1, 1, 1, 1, 28, 1, 1, 1, 1] 168
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 283
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043781 none CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
168  conformations in input
total number of sets (complete confs): 168
using faster count positions algorithm for large data
unique positions, atoms: [168, 158, 135, 88, 28, 88, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 168, 168, 168, 168, 168, 158, 158, 135, 135, 28, 28, 28, 28, 1, 28, 28, 28, 28] 168
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 652
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043781 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043781
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043781/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043781
Building REAL250005043782
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043782'
/scratch/stefan/7916125/working/building/REAL250005043782 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043782

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043782/0 /scratch/stefan/7916125/working/building/REAL250005043782 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/898
`/scratch/stefan/7916125/working/3D/898' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043782 none CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [17, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 30, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 106
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043782 none CC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 30, 71, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 71, 71, 71, 71, 71, 71, 71, 30, 30, 30, 30, 1, 30, 30, 30, 30] 71
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 174
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043782 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043782
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043782/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043782
Building REAL250005043783
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043783'
/scratch/stefan/7916125/working/building/REAL250005043783 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043783

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043783/0 /scratch/stefan/7916125/working/building/REAL250005043783 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/899
`/scratch/stefan/7916125/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043783 none CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 32, 32, 32, 32, 32, 18, 18, 18, 18, 1, 1, 1, 1, 35, 1, 1, 1, 1] 128
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 213
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043783 none CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 121, 95, 121, 35, 95, 35, 35, 35, 11, 1, 11, 1, 1, 1, 1, 1, 1, 35, 35, 128, 128, 128, 128, 128, 121, 121, 121, 121, 35, 35, 35, 35, 1, 35, 35, 35, 35] 128
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 418
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043783 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043783
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043783/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043783
Building REAL250005043784
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043784'
/scratch/stefan/7916125/working/building/REAL250005043784 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043784

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043784/0 /scratch/stefan/7916125/working/building/REAL250005043784 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/900
`/scratch/stefan/7916125/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043784 none CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [20, 13, 7, 13, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 22, 22, 22, 22, 22, 13, 22, 22, 22, 22, 22, 1, 1, 1, 1, 30, 1, 1, 1, 1] 173
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 214
number of broken/clashed sets: 104
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043784 none CCC(CC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
173  conformations in input
total number of sets (complete confs): 173
using faster count positions algorithm for large data
unique positions, atoms: [155, 137, 118, 137, 157, 30, 118, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 157, 157, 157, 157, 157, 137, 159, 159, 159, 159, 159, 30, 30, 30, 30, 1, 30, 30, 30, 30] 173
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 665
number of broken/clashed sets: 104
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043784 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043784
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043784/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043784
Building REAL250005043785
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043785'
/scratch/stefan/7916125/working/building/REAL250005043785 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043785

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043785/0 /scratch/stefan/7916125/working/building/REAL250005043785 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/901
`/scratch/stefan/7916125/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 36, 36, 36, 36, 104, 104, 124, 124, 124, 124, 124, 36, 36, 1, 1, 1, 36, 36, 36, 36, 124, 36, 36, 36, 36] 124
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 290
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 36, 36, 36, 36, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 36, 36, 36, 1, 1, 1, 1, 33, 1, 1, 1, 1] 124
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 96
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=NNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
124  conformations in input
total number of sets (complete confs): 124
using faster count positions algorithm for large data
unique positions, atoms: [93, 33, 91, 124, 124, 124, 124, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 124, 124, 124, 33, 33, 33, 33, 1, 33, 33, 33, 33] 124
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 288
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043785 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043785/1 /scratch/stefan/7916125/working/building/REAL250005043785 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/902
`/scratch/stefan/7916125/working/3D/902' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043785.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043785/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 11, 25, 25, 25, 25, 76, 76, 99, 99, 99, 99, 99, 25, 25, 1, 1, 1, 25, 25, 25, 25, 99, 25, 25, 25, 25] 99
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 231
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 25, 25, 25, 25, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 25, 25, 25, 1, 1, 1, 1, 30, 1, 1, 1, 1] 99
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 82
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043785 none O=C(C1=CC=NN1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [69, 30, 69, 99, 99, 99, 99, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 99, 99, 99, 30, 30, 30, 30, 1, 30, 30, 30, 30] 99
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 226
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043785 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043785
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043785/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043785/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043785
Building REAL250005043786
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043786'
/scratch/stefan/7916125/working/building/REAL250005043786 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043786

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043786/0 /scratch/stefan/7916125/working/building/REAL250005043786 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/903
`/scratch/stefan/7916125/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043786 none CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [58, 15, 6, 15, 1, 6, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 56, 58, 58, 15, 15, 15, 15, 1, 1, 1, 1, 38, 1, 1, 1, 1] 174
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 167
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043786 none CSC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
174  conformations in input
total number of sets (complete confs): 174
using faster count positions algorithm for large data
unique positions, atoms: [174, 128, 109, 128, 32, 109, 38, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 174, 174, 174, 128, 128, 128, 128, 38, 38, 38, 38, 1, 38, 38, 38, 38] 174
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 469
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043786 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043786
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043786/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043786
Building REAL250005043787
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043787'
/scratch/stefan/7916125/working/building/REAL250005043787 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043787

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043787/0 /scratch/stefan/7916125/working/building/REAL250005043787 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/904
`/scratch/stefan/7916125/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043787 none CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 36, 18, 6, 18, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 37, 37, 37, 37, 37, 18, 18, 18, 18, 1, 1, 1, 1, 36, 1, 1, 1, 1] 142
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 149
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043787 none CCOC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [142, 142, 119, 92, 119, 36, 93, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 142, 142, 142, 142, 142, 119, 119, 119, 119, 36, 36, 36, 36, 1, 36, 36, 36, 36] 142
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 423
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043787 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043787
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043787/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043787
Building REAL250005043788
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043788'
/scratch/stefan/7916125/working/building/REAL250005043788 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043788

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043788/0 /scratch/stefan/7916125/working/building/REAL250005043788 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/905
`/scratch/stefan/7916125/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043788 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 39, 39, 55, 55, 55, 55, 55, 15, 15, 1, 1, 1, 15, 15, 15, 15, 55, 15, 15, 15, 15] 55
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 123
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043788 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 14, 14, 14, 14, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 14, 14, 14, 1, 1, 1, 1, 28, 1, 1, 1, 1] 54
rigid atoms, others: [32, 1, 7, 8, 9, 10, 11, 19, 20, 24, 25, 26, 27, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28])
total number of confs: 68
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043788 none O=C(C1=CNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 28, 54, 54, 54, 54, 54, 28, 28, 28, 11, 1, 11, 1, 1, 1, 1, 1, 1, 28, 28, 54, 54, 54, 28, 28, 28, 28, 1, 28, 28, 28, 28] 54
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 128
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043788 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043788
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043788/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043788
Building REAL250005043789
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043789'
/scratch/stefan/7916125/working/building/REAL250005043789 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043789

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043789/0 /scratch/stefan/7916125/working/building/REAL250005043789 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/906
`/scratch/stefan/7916125/working/3D/906' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043789 none COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 64, 30, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 111, 111, 111, 63, 63, 32, 32, 18, 18, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 419
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043789 none COCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 114, 81, 53, 15, 53, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 199, 200, 120, 120, 81, 81, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 922
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043789 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043789
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043789/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043789
Building REAL250005043790
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043790'
/scratch/stefan/7916125/working/building/REAL250005043790 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043790

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043790/0 /scratch/stefan/7916125/working/building/REAL250005043790 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/907
`/scratch/stefan/7916125/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1)

`REAL250005043790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043790 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 93, 93, 131, 131, 131, 131, 33, 33, 1, 33, 33, 33, 33, 131, 131, 33, 33, 33, 33] 131
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 291
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043790 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39, 1, 1, 33, 1, 1, 1, 1, 39, 39, 1, 1, 1, 1] 131
rigid atoms, others: [1, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27])
total number of confs: 99
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043790 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2=NOC=C2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [103, 39, 103, 131, 131, 131, 131, 131, 39, 39, 39, 12, 1, 12, 1, 1, 1, 1, 1, 39, 39, 131, 39, 39, 39, 39, 1, 1, 39, 39, 39, 39] 131
rigid atoms, others: [12, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31])
total number of confs: 301
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043790 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043790
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043790/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043790
Building REAL250005043791
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043791'
/scratch/stefan/7916125/working/building/REAL250005043791 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043791

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043791/0 /scratch/stefan/7916125/working/building/REAL250005043791 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/908
`/scratch/stefan/7916125/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043791 none CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [60, 30, 30, 7, 30, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 60, 60, 60, 60, 60, 30, 30, 30, 30, 1, 1, 1, 1, 33, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 263
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043791 none CCC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 184, 113, 184, 33, 113, 33, 33, 32, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 184, 184, 184, 184, 33, 33, 33, 33, 1, 33, 33, 33, 33] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 621
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043791 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043791
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043791/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043791
Building REAL250005043792
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043792'
/scratch/stefan/7916125/working/building/REAL250005043792 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043792

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043792/0 /scratch/stefan/7916125/working/building/REAL250005043792 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/909
`/scratch/stefan/7916125/working/3D/909' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043792 none COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [34, 21, 6, 21, 1, 6, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 34, 34, 34, 21, 21, 21, 21, 1, 1, 1, 1, 35, 1, 1, 1, 1] 115
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 146
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043792 none COC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
115  conformations in input
total number of sets (complete confs): 115
using faster count positions algorithm for large data
unique positions, atoms: [115, 112, 95, 112, 35, 95, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 115, 115, 115, 112, 112, 112, 112, 35, 35, 35, 35, 1, 35, 35, 35, 35] 115
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 336
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043792 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043792
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043792/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043792
Building REAL250005043793
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043793'
/scratch/stefan/7916125/working/building/REAL250005043793 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043793

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043793/0 /scratch/stefan/7916125/working/building/REAL250005043793 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/910
`/scratch/stefan/7916125/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043793 none CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 68, 90, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 90, 90, 90, 90, 90, 90, 90, 22, 22, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 300
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043793 none CC(C)OCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 201, 99, 50, 15, 50, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 201, 201, 201, 201, 99, 99, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 645
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043793 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043793
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043793/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043793
Building REAL250005043794
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043794'
/scratch/stefan/7916125/working/building/REAL250005043794 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043794

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043794/0 /scratch/stefan/7916125/working/building/REAL250005043794 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/911
`/scratch/stefan/7916125/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043794 none CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 66, 40, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 91, 91, 91, 91, 91, 66, 66, 18, 18, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 383
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043794 none CCCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 173, 134, 82, 39, 13, 39, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 173, 173, 82, 82, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 768
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043794 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043794
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043794/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043794
Building REAL250005043795
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043795'
/scratch/stefan/7916125/working/building/REAL250005043795 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043795

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043795/0 /scratch/stefan/7916125/working/building/REAL250005043795 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/912
`/scratch/stefan/7916125/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1)

`REAL250005043795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043795 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 75, 75, 99, 99, 99, 99, 30, 30, 1, 30, 30, 30, 30, 98, 99, 99, 99, 99, 99, 99, 30, 30, 30, 30] 99
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 285
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043795 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 1, 1, 30, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1] 99
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 100
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: REAL250005043795 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCOC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
99  conformations in input
total number of sets (complete confs): 99
using faster count positions algorithm for large data
unique positions, atoms: [73, 22, 75, 99, 99, 99, 99, 99, 22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 22, 22, 99, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22] 99
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 222
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043795 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043795
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043795/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043795
Building REAL250005043796
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043796'
/scratch/stefan/7916125/working/building/REAL250005043796 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043796

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043796/0 /scratch/stefan/7916125/working/building/REAL250005043796 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/913
`/scratch/stefan/7916125/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043796 none CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 24, 7, 24, 35, 1, 7, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 41, 41, 41, 41, 41, 24, 35, 35, 35, 1, 1, 1, 1, 30, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 264
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043796 none CCC(OC)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 188, 106, 188, 198, 30, 106, 30, 30, 30, 10, 1, 10, 1, 1, 1, 1, 1, 1, 30, 30, 198, 198, 198, 198, 198, 188, 198, 198, 198, 30, 30, 30, 30, 1, 30, 30, 30, 30] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 779
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043796 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043796
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043796/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043796
Building REAL250005043797
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043797'
/scratch/stefan/7916125/working/building/REAL250005043797 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043797

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043797/0 /scratch/stefan/7916125/working/building/REAL250005043797 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/914
`/scratch/stefan/7916125/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043797 none COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 60, 31, 60, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 79, 79, 79, 60, 60, 60, 60, 31, 31, 1, 1, 1, 1, 26, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 328
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043797 none COC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 166, 200, 88, 26, 88, 26, 26, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 26, 26, 201, 201, 201, 200, 200, 200, 200, 166, 166, 26, 26, 26, 26, 1, 26, 26, 26, 26] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 779
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043797 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043797
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043797/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043797
Building REAL250005043798
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043798'
/scratch/stefan/7916125/working/building/REAL250005043798 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043798

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043798/0 /scratch/stefan/7916125/working/building/REAL250005043798 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/915
`/scratch/stefan/7916125/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043798 none C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [69, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 69, 69, 69, 26, 26, 16, 16, 1, 1, 1, 1, 33, 1, 1, 1, 1] 164
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 283
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043798 none C=CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 145, 103, 33, 103, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 164, 164, 164, 164, 164, 145, 145, 33, 33, 33, 33, 1, 33, 33, 33, 33] 164
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 585
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043798 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043798
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043798/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043798
Building REAL250005043799
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043799'
/scratch/stefan/7916125/working/building/REAL250005043799 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043799

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043799/0 /scratch/stefan/7916125/working/building/REAL250005043799 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/916
`/scratch/stefan/7916125/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043799 none CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 37, 21, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 99, 99, 99, 98, 98, 37, 37, 21, 21, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 356
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043799 none CCOCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 148, 114, 75, 19, 75, 19, 19, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 201, 201, 148, 148, 114, 114, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 644
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043799 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043799
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043799/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043799
Building REAL250005043800
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043800'
/scratch/stefan/7916125/working/building/REAL250005043800 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043800

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043800/0 /scratch/stefan/7916125/working/building/REAL250005043800 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/917
`/scratch/stefan/7916125/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043800 none COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 102, 102, 102, 61, 61, 19, 19, 19, 19, 1, 1, 1, 1, 23, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 346
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043800 none COCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 138, 89, 138, 23, 89, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 201, 201, 201, 201, 201, 138, 138, 138, 138, 23, 23, 23, 23, 1, 23, 23, 23, 23] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 830
number of broken/clashed sets: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043800 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043800
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043800/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043800
Building REAL250005043801
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043801'
/scratch/stefan/7916125/working/building/REAL250005043801 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043801

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043801/0 /scratch/stefan/7916125/working/building/REAL250005043801 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/918
`/scratch/stefan/7916125/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043801 none C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 83, 37, 15, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 99, 99, 99, 83, 83, 15, 15, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 384
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043801 none C=CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 79, 49, 13, 49, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 201, 201, 79, 79, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 727
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043801 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043801
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043801/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043801
Building REAL250005043802
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043802'
/scratch/stefan/7916125/working/building/REAL250005043802 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043802

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043802/0 /scratch/stefan/7916125/working/building/REAL250005043802 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/919
`/scratch/stefan/7916125/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043802 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 93, 93, 111, 111, 111, 111, 111, 34, 34, 1, 1, 34, 34, 34, 34, 111, 34, 34, 34, 34] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 259
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043802 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 34, 34, 34, 34, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 34, 34, 1, 1, 1, 1, 33, 1, 1, 1, 1] 111
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043802 none O=C(C1=COC=N1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 12, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [85, 33, 85, 111, 111, 111, 111, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 111, 111, 33, 33, 33, 33, 1, 33, 33, 33, 33] 111
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 251
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043802 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043802
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043802/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043802
Building REAL250005043803
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043803'
/scratch/stefan/7916125/working/building/REAL250005043803 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043803

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043803/0 /scratch/stefan/7916125/working/building/REAL250005043803 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/920
`/scratch/stefan/7916125/working/3D/920' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043803 none CC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 19, 19, 19, 19, 1, 1, 1, 1, 37, 1, 1, 1, 1] 98
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 18, 19, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28])
total number of confs: 119
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043803 none CC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
98  conformations in input
total number of sets (complete confs): 98
using faster count positions algorithm for large data
unique positions, atoms: [98, 84, 98, 98, 36, 84, 37, 37, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 98, 98, 98, 98, 37, 37, 37, 37, 1, 37, 37, 37, 37] 98
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 293
number of broken/clashed sets: 34
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043803 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043803
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043803/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043803
Building REAL250005043804
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043804'
/scratch/stefan/7916125/working/building/REAL250005043804 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043804

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043804/0 /scratch/stefan/7916125/working/building/REAL250005043804 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/921
`/scratch/stefan/7916125/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043804 none CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 59, 59, 59, 59, 56, 52, 52, 19, 19, 19, 19, 1, 1, 1, 1, 31, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 304
number of broken/clashed sets: 102
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043804 none CCCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 169, 118, 169, 31, 118, 31, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 201, 201, 201, 201, 197, 201, 201, 169, 169, 169, 169, 31, 31, 31, 31, 1, 31, 31, 31, 31] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 769
number of broken/clashed sets: 102
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043804 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043804
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043804/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043804
Building REAL250005043805
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043805'
/scratch/stefan/7916125/working/building/REAL250005043805 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043805

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043805/0 /scratch/stefan/7916125/working/building/REAL250005043805 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/922
`/scratch/stefan/7916125/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043805 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 7, 3, 1, 1, 1, 1, 31, 60, 60, 60, 60, 177, 177, 201, 201, 201, 201, 201, 60, 60, 7, 7, 3, 3, 1, 1, 1, 1, 1, 60, 60, 60, 60, 201, 60, 60, 60, 60] 201
rigid atoms, others: [3, 4, 5, 6, 25, 26, 27, 28, 29] set([0, 1, 2, 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])
total number of confs: 490
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043805 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 36, 60, 60, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 20, 20, 38, 38, 60, 60, 60, 60, 60, 1, 1, 1, 1, 29, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 35, 36, 33, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 305
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: REAL250005043805 none O=C(CCC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 29, 84, 135, 151, 201, 201, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 29, 29, 135, 135, 153, 153, 201, 201, 201, 201, 201, 29, 29, 29, 29, 1, 29, 29, 29, 29] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 763
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043805 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043805
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043805/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043805
Building REAL250005043806
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043806'
/scratch/stefan/7916125/working/building/REAL250005043806 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043806

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043806/0 /scratch/stefan/7916125/working/building/REAL250005043806 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/923
`/scratch/stefan/7916125/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1)

`REAL250005043806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043806 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 64, 64, 93, 93, 93, 93, 28, 28, 1, 28, 28, 28, 28, 93, 93, 93, 93, 93, 93, 93, 28, 28, 28, 28] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 271
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043806 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 1, 1, 28, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 93
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 88
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: REAL250005043806 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC=CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', '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, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [69, 17, 69, 93, 93, 93, 93, 93, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 17, 17, 93, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 93
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 207
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043806 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043806
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043806/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043806
Building REAL250005043807
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043807'
/scratch/stefan/7916125/working/building/REAL250005043807 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043807

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043807/0 /scratch/stefan/7916125/working/building/REAL250005043807 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/924
`/scratch/stefan/7916125/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043807 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [26, 6, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 148, 148, 177, 177, 177, 177, 177, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 177, 50, 50, 50, 50] 177
rigid atoms, others: [2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 430
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043807 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 27, 50, 50, 50, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 27, 27, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 36, 1, 1, 1, 1] 177
rigid atoms, others: [32, 1, 35, 36, 33, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 211
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: REAL250005043807 none O=C(CC1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
177  conformations in input
total number of sets (complete confs): 177
using faster count positions algorithm for large data
unique positions, atoms: [106, 36, 106, 140, 177, 177, 177, 36, 36, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 140, 140, 177, 177, 177, 177, 177, 177, 177, 36, 36, 36, 36, 1, 36, 36, 36, 36] 177
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 589
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043807 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043807
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043807/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043807
Building REAL250005043808
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043808'
/scratch/stefan/7916125/working/building/REAL250005043808 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043808

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043808/0 /scratch/stefan/7916125/working/building/REAL250005043808 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/925
`/scratch/stefan/7916125/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1)

`REAL250005043808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043808 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 16, 22, 22, 16, 16, 16, 16, 1, 1, 1, 1, 33, 1, 1, 1, 1, 22, 22, 22, 22, 22] 94
rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 16, 17, 25, 26, 27, 28, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38])
total number of confs: 130
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043808 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 75, 33, 75, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 94, 94, 94, 94, 94, 94, 94, 33, 33, 33, 33, 1, 33, 33, 33, 33, 94, 94, 94, 94, 94] 94
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 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: 295
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: REAL250005043808 none CC(C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 11, 11, 22, 22, 22, 22, 69, 69, 94, 94, 94, 94, 94, 22, 22, 1, 1, 1, 4, 4, 4, 3, 22, 22, 22, 22, 94, 22, 22, 22, 22, 1, 1, 1, 1, 1] 94
rigid atoms, others: [1, 34, 35, 36, 37, 38, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 226
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043808 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043808
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043808/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043808
Building REAL250005043809
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043809'
/scratch/stefan/7916125/working/building/REAL250005043809 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043809

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043809/0 /scratch/stefan/7916125/working/building/REAL250005043809 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/926
`/scratch/stefan/7916125/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043809 none CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 7, 28, 1, 7, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 32, 1, 1, 1, 1] 108
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 114
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043809 none CC=C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 108, 64, 108, 32, 64, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 108, 108, 108, 108, 108, 108, 108, 32, 32, 32, 32, 1, 32, 32, 32, 32] 108
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 336
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043809 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043809
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043809/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043809
Building REAL250005043810
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043810'
/scratch/stefan/7916125/working/building/REAL250005043810 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043810

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043810/0 /scratch/stefan/7916125/working/building/REAL250005043810 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/927
`/scratch/stefan/7916125/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1)

`REAL250005043810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043810 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 85, 85, 105, 105, 105, 105, 105, 23, 23, 1, 2, 2, 2, 1, 1, 1, 1, 23, 23, 23, 23, 105, 23, 23, 23, 23, 1, 1] 105
rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 239
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043810 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 33, 1, 1, 1, 1, 23, 23] 105
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 32, 37, 38])
total number of confs: 105
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: REAL250005043810 none CC1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 89, 33, 89, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 105, 105, 105, 105, 105, 105, 105, 105, 33, 33, 33, 33, 1, 33, 33, 33, 33, 105, 105] 105
rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38])
total number of confs: 283
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043810 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043810
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043810/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043810
Building REAL250005043811
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043811'
/scratch/stefan/7916125/working/building/REAL250005043811 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043811

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043811/0 /scratch/stefan/7916125/working/building/REAL250005043811 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/928
`/scratch/stefan/7916125/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043811 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 10, 44, 44, 44, 44, 149, 149, 187, 187, 187, 187, 187, 44, 43, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 187, 44, 44, 44, 44] 187
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 429
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043811 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 44, 44, 44, 44, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 40, 40, 1, 1, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 40, 1, 1, 1, 1] 187
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 154
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: REAL250005043811 none O=C(C=C1CCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
187  conformations in input
total number of sets (complete confs): 187
using faster count positions algorithm for large data
unique positions, atoms: [118, 40, 118, 187, 187, 187, 187, 40, 40, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 40, 40, 187, 187, 187, 187, 187, 187, 187, 40, 40, 40, 40, 1, 40, 40, 40, 40] 187
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 520
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043811 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043811
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043811/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043811
Building REAL250005043812
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043812'
/scratch/stefan/7916125/working/building/REAL250005043812 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043812

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043812/0 /scratch/stefan/7916125/working/building/REAL250005043812 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/929
`/scratch/stefan/7916125/working/3D/929' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043812 none CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 25, 7, 25, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 37, 1, 1, 1, 1] 103
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043812 none CC(C)=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [103, 103, 103, 77, 103, 31, 75, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 103, 103, 103, 103, 103, 103, 37, 37, 37, 37, 1, 37, 37, 37, 37] 103
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043812 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043812
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043812/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043812
Building REAL250005043813
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043813'
/scratch/stefan/7916125/working/building/REAL250005043813 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043813

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043813/0 /scratch/stefan/7916125/working/building/REAL250005043813 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/930
`/scratch/stefan/7916125/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043813 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 62, 62, 78, 78, 78, 78, 78, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 78, 24, 24, 24, 24] 78
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 174
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043813 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 37, 1, 1, 1, 1] 78
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 88
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: REAL250005043813 none O=C(C1=CCCC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
78  conformations in input
total number of sets (complete confs): 78
using faster count positions algorithm for large data
unique positions, atoms: [78, 37, 78, 78, 78, 78, 78, 37, 37, 37, 12, 1, 12, 1, 1, 1, 1, 1, 1, 37, 37, 78, 78, 78, 78, 78, 78, 78, 37, 37, 37, 37, 1, 37, 37, 37, 37] 78
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 189
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043813 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043813
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043813/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043813
Building REAL250005043814
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043814'
/scratch/stefan/7916125/working/building/REAL250005043814 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043814

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043814/0 /scratch/stefan/7916125/working/building/REAL250005043814 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/931
`/scratch/stefan/7916125/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043814 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 57, 57, 71, 71, 71, 71, 71, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 71, 17, 17, 17, 17] 71
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 168
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043814 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 29, 1, 1, 1, 1] 71
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 89
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: REAL250005043814 none CC1(C)CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
71  conformations in input
total number of sets (complete confs): 71
using faster count positions algorithm for large data
unique positions, atoms: [71, 71, 71, 71, 69, 29, 69, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 71, 71, 71, 71, 71, 71, 71, 71, 71, 29, 29, 29, 29, 1, 29, 29, 29, 29] 71
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 169
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043814 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043814
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043814/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043814
Building REAL250005043815
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043815'
/scratch/stefan/7916125/working/building/REAL250005043815 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043815

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043815/0 /scratch/stefan/7916125/working/building/REAL250005043815 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/932
`/scratch/stefan/7916125/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043815 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 61, 61, 75, 75, 75, 75, 75, 20, 20, 2, 2, 2, 2, 2, 2, 1, 1, 20, 20, 20, 20, 75, 20, 20, 20, 20] 75
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])
total number of confs: 183
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043815 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 6, 20, 1, 6, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 26, 1, 1, 1, 1] 75
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 92
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: REAL250005043815 none CC1(C)C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
75  conformations in input
total number of sets (complete confs): 75
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 75, 68, 75, 26, 68, 26, 26, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 26, 26, 75, 75, 75, 75, 75, 75, 75, 75, 26, 26, 26, 26, 1, 26, 26, 26, 26] 75
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 193
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043815 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043815
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043815/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043815
Building REAL250005043816
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043816'
/scratch/stefan/7916125/working/building/REAL250005043816 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043816

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043816/0 /scratch/stefan/7916125/working/building/REAL250005043816 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/933
`/scratch/stefan/7916125/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1)

`REAL250005043816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043816 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 79, 79, 97, 97, 97, 97, 97, 28, 28, 1, 28, 28, 28, 28, 97, 97, 97, 97, 97, 97, 28, 28, 28, 28] 97
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 256
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043816 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 28, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 97
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29, 30, 31])
total number of confs: 98
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: REAL250005043816 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [81, 23, 81, 97, 97, 97, 97, 97, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 97, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 97
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 222
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043816 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043816
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043816/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043816
Building REAL250005043817
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043817'
/scratch/stefan/7916125/working/building/REAL250005043817 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043817

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043817/0 /scratch/stefan/7916125/working/building/REAL250005043817 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/934
`/scratch/stefan/7916125/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043817 none CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 46, 25, 46, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 20, 1, 1, 61, 61, 61, 61, 61, 46, 46, 46, 46, 25, 25, 1, 1, 1, 1, 20, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 307
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043817 none CCC(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 153, 190, 84, 20, 84, 20, 20, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 20, 20, 201, 201, 201, 201, 201, 190, 190, 190, 190, 153, 153, 20, 20, 20, 20, 1, 20, 20, 20, 20] 201
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 832
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043817 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043817
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043817/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043817
Building REAL250005043818
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043818'
/scratch/stefan/7916125/working/building/REAL250005043818 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043818

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043818/0 /scratch/stefan/7916125/working/building/REAL250005043818 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/935
`/scratch/stefan/7916125/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043818 none C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 56, 55, 55, 28, 28, 16, 16, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 303
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043818 none C#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 113, 87, 49, 17, 49, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 201, 200, 200, 115, 115, 87, 87, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 932
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043818 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043818
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043818/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043818
Building REAL250005043819
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043819'
/scratch/stefan/7916125/working/building/REAL250005043819 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043819

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043819/0 /scratch/stefan/7916125/working/building/REAL250005043819 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/936
`/scratch/stefan/7916125/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043819 none CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
249  conformations in input
total number of sets (complete confs): 249
using faster count positions algorithm for large data
unique positions, atoms: [24, 21, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 30, 30, 30, 30, 30, 1, 1, 24, 24, 24, 24, 24, 24, 72, 21, 21, 1, 1, 1, 1, 30, 1, 1, 1, 1] 249
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 209
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043819 none CC(C)(O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
249  conformations in input
total number of sets (complete confs): 249
using faster count positions algorithm for large data
unique positions, atoms: [83, 82, 83, 83, 70, 30, 70, 30, 30, 30, 12, 1, 12, 1, 1, 1, 1, 1, 1, 30, 30, 83, 83, 83, 83, 83, 83, 249, 82, 82, 30, 30, 30, 30, 1, 30, 30, 30, 30] 249
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 492
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043819 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043819
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043819/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043819
Building REAL250005043820
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043820'
/scratch/stefan/7916125/working/building/REAL250005043820 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043820

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043820/0 /scratch/stefan/7916125/working/building/REAL250005043820 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/937
`/scratch/stefan/7916125/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043820 none CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [35, 22, 34, 7, 22, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 35, 35, 35, 35, 35, 35, 35, 66, 1, 1, 1, 1, 27, 1, 1, 1, 1] 372
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 265
number of broken/clashed sets: 136
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043820 none CC(C)[C@@H](O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
372  conformations in input
total number of sets (complete confs): 372
using faster count positions algorithm for large data
unique positions, atoms: [124, 113, 124, 81, 113, 113, 27, 81, 27, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 124, 124, 124, 124, 124, 124, 124, 339, 27, 27, 27, 27, 1, 27, 27, 27, 27] 372
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 780
number of broken/clashed sets: 136
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043820 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043820
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043820/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043820
Building REAL250005043821
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043821'
/scratch/stefan/7916125/working/building/REAL250005043821 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043821

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043821/0 /scratch/stefan/7916125/working/building/REAL250005043821 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/938
`/scratch/stefan/7916125/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043821 none CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [42, 22, 22, 22, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 42, 42, 42, 42, 42, 22, 22, 22, 22, 1, 1, 1, 1, 36, 1, 1, 1, 1] 176
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 223
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043821 none CCC(C)=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
176  conformations in input
total number of sets (complete confs): 176
using faster count positions algorithm for large data
unique positions, atoms: [176, 122, 122, 122, 88, 36, 88, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 176, 176, 176, 176, 176, 122, 122, 122, 122, 36, 36, 36, 36, 1, 36, 36, 36, 36] 176
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 664
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043821 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043821
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043821/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043821
Building REAL250005043822
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043822'
/scratch/stefan/7916125/working/building/REAL250005043822 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043822

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043822/0 /scratch/stefan/7916125/working/building/REAL250005043822 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/939
`/scratch/stefan/7916125/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043822 none CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 6, 6, 6, 6, 1, 1, 1, 1, 29, 1, 1, 1, 1] 47
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 61
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043822 none CC(C)C#CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 47, 47, 29, 47, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 1, 29, 29, 29, 29] 47
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 121
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043822 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043822
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043822/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043822
Building REAL250005043823
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043823'
/scratch/stefan/7916125/working/building/REAL250005043823 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043823

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043823/0 /scratch/stefan/7916125/working/building/REAL250005043823 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/940
`/scratch/stefan/7916125/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043823 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 37, 37, 55, 55, 55, 55, 55, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 55, 6, 6, 6, 6] 55
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 115
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043823 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 29, 1, 1, 1, 1] 55
rigid atoms, others: [32, 1, 34, 33, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 57
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043823 none O=C(C#CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 29, 55, 55, 55, 55, 55, 29, 29, 29, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 55, 55, 55, 55, 55, 29, 29, 29, 29, 1, 29, 29, 29, 29] 55
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 141
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043823 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043823
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043823/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043823
Building REAL250005043824
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043824'
/scratch/stefan/7916125/working/building/REAL250005043824 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043824

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043824/0 /scratch/stefan/7916125/working/building/REAL250005043824 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/941
`/scratch/stefan/7916125/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043824 none CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 17, 17, 17, 16, 16, 1, 1, 1, 1, 27, 1, 1, 1, 1] 61
rigid atoms, others: [2, 4, 5, 6, 7, 8, 16, 17, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 27])
total number of confs: 107
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043824 none CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
61  conformations in input
total number of sets (complete confs): 61
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 27, 61, 27, 27, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 27, 27, 61, 61, 61, 61, 61, 27, 27, 27, 27, 1, 27, 27, 27, 27] 61
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 158
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043824 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043824
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043824/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043824
Building REAL250005043825
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043825'
/scratch/stefan/7916125/working/building/REAL250005043825 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043825

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043825/0 /scratch/stefan/7916125/working/building/REAL250005043825 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/942
`/scratch/stefan/7916125/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043825 none COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [63, 33, 19, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 63, 63, 63, 33, 33, 19, 19, 1, 1, 1, 1, 29, 1, 1, 1, 1] 143
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 234
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043825 none COCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
143  conformations in input
total number of sets (complete confs): 143
using faster count positions algorithm for large data
unique positions, atoms: [143, 141, 111, 84, 29, 84, 29, 29, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 29, 143, 143, 143, 141, 141, 111, 111, 29, 29, 29, 29, 1, 29, 29, 29, 29] 143
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 534
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043825 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043825
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043825/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043825
Building REAL250005043826
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043826'
/scratch/stefan/7916125/working/building/REAL250005043826 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043826

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043826/0 /scratch/stefan/7916125/working/building/REAL250005043826 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/943
`/scratch/stefan/7916125/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1)

`REAL250005043826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043826 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 26, 26, 26, 26, 44, 44, 65, 65, 26, 26, 1, 26, 26, 26, 26, 65, 65, 65, 65, 65, 26, 26, 26, 26] 65
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 19] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 194
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043826 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 6, 6, 17, 17, 1, 1, 26, 1, 1, 1, 1, 17, 17, 17, 17, 17, 1, 1, 1, 1] 65
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 17, 18, 20, 21, 22, 23, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 19, 24, 25, 26, 27, 28])
total number of confs: 86
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043826 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
65  conformations in input
total number of sets (complete confs): 65
using faster count positions algorithm for large data
unique positions, atoms: [53, 17, 53, 65, 65, 65, 65, 65, 17, 17, 17, 8, 1, 8, 1, 1, 1, 17, 17, 65, 17, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17] 65
rigid atoms, others: [12, 14, 15, 16, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32])
total number of confs: 157
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043826 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043826
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043826/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043826
Building REAL250005043827
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043827'
/scratch/stefan/7916125/working/building/REAL250005043827 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043827

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043827/0 /scratch/stefan/7916125/working/building/REAL250005043827 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/944
`/scratch/stefan/7916125/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1)

`REAL250005043827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043827 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 29, 29, 29, 29, 71, 71, 93, 93, 93, 29, 29, 1, 29, 29, 29, 29, 93, 93, 93, 93, 93, 93, 93, 29, 29, 29, 29] 93
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 259
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043827 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 1, 1, 29, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 93
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 97
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: REAL250005043827 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [73, 21, 73, 93, 93, 93, 93, 93, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 21, 21, 93, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 93
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35])
total number of confs: 215
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043827 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043827
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043827/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043827
Building REAL250005043828
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043828'
/scratch/stefan/7916125/working/building/REAL250005043828 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043828

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043828/0 /scratch/stefan/7916125/working/building/REAL250005043828 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/945
`/scratch/stefan/7916125/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1)

`REAL250005043828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043828 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 79, 79, 101, 101, 101, 101, 30, 30, 1, 30, 30, 30, 30, 101, 101, 101, 101, 101, 101, 101, 101, 101, 30, 30, 30, 30] 101
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 286
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043828 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 1, 1, 30, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 101
rigid atoms, others: [1, 35, 36, 37, 38, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 98
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: REAL250005043828 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCCC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
101  conformations in input
total number of sets (complete confs): 101
using faster count positions algorithm for large data
unique positions, atoms: [73, 21, 73, 101, 101, 101, 101, 101, 21, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 21, 21, 101, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 101
rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38])
total number of confs: 220
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043828 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043828
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043828/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043828
Building REAL250005043829
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043829'
/scratch/stefan/7916125/working/building/REAL250005043829 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043829

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043829/0 /scratch/stefan/7916125/working/building/REAL250005043829 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/946
`/scratch/stefan/7916125/working/3D/946' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043829 none C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 32, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 1, 1, 104, 104, 104, 59, 59, 34, 34, 18, 18, 1, 1, 1, 1, 15, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 456
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043829 none C=CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 112, 79, 53, 15, 53, 15, 15, 15, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 201, 201, 201, 199, 199, 116, 116, 79, 79, 15, 15, 15, 15, 1, 15, 15, 15, 15] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 918
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043829 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043829
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043829/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043829
Building REAL250005043830
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043830'
/scratch/stefan/7916125/working/building/REAL250005043830 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043830

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043830/0 /scratch/stefan/7916125/working/building/REAL250005043830 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/947
`/scratch/stefan/7916125/working/3D/947' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043830 none CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 3, 7, 7, 1, 3, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 1, 1, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 23, 1, 1, 1, 1] 114
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 103
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043830 none CCC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
114  conformations in input
total number of sets (complete confs): 114
using faster count positions algorithm for large data
unique positions, atoms: [114, 112, 39, 112, 112, 23, 39, 23, 23, 23, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 23, 114, 114, 114, 114, 114, 112, 112, 112, 112, 112, 112, 23, 23, 23, 23, 1, 23, 23, 23, 23] 114
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 454
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043830 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043830
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043830/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043830
Building REAL250005043831
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043831'
/scratch/stefan/7916125/working/building/REAL250005043831 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043831

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043831/0 /scratch/stefan/7916125/working/building/REAL250005043831 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/948
`/scratch/stefan/7916125/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043831 none NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [29, 7, 29, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 29, 29, 1, 1, 1, 1, 27, 1, 1, 1, 1] 83
rigid atoms, others: [3, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 25])
total number of confs: 111
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043831 none NC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 63, 83, 27, 63, 27, 27, 26, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 83, 83, 27, 27, 27, 27, 1, 27, 27, 27, 27] 83
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 236
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043831 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043831
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043831/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043831
Building REAL250005043832
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043832'
/scratch/stefan/7916125/working/building/REAL250005043832 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043832

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043832/0 /scratch/stefan/7916125/working/building/REAL250005043832 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/949
`/scratch/stefan/7916125/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043832 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 35, 35, 67, 67, 67, 67, 188, 188, 201, 201, 201, 201, 201, 67, 67, 2, 2, 2, 1, 1, 1, 1, 7, 7, 67, 67, 67, 67, 201, 67, 67, 67, 67] 201
rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 510
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043832 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 29, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 67, 67, 67, 67, 67, 67, 67, 29, 29, 1, 1, 1, 1, 24, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 259
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: REAL250005043832 none CC1CC1CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 159, 78, 24, 78, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 201, 201, 201, 201, 201, 201, 201, 159, 159, 24, 24, 24, 24, 1, 24, 24, 24, 24] 201
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 724
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043832 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043832
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043832/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043832
Building REAL250005043833
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043833'
/scratch/stefan/7916125/working/building/REAL250005043833 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043833

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043833/0 /scratch/stefan/7916125/working/building/REAL250005043833 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/950
`/scratch/stefan/7916125/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043833 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 5, 5, 8, 8, 8, 8, 37, 37, 70, 70, 70, 70, 70, 8, 8, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 70, 8, 8, 8, 8, 1, 1, 1, 1] 80
rigid atoms, others: [1, 2, 3, 36, 37, 35, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 153
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043833 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 1, 1, 8, 8, 14, 14, 14, 14, 14, 1, 1, 1, 1, 24, 1, 1, 1, 1, 8, 8, 8, 8] 80
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043833 none CCC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 58, 24, 58, 24, 24, 24, 10, 1, 10, 1, 1, 1, 1, 1, 1, 24, 24, 70, 70, 80, 80, 80, 80, 80, 24, 24, 24, 24, 1, 24, 24, 24, 24, 70, 70, 70, 70] 80
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043833 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043833
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043833/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043833
Building REAL250005043834
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043834'
/scratch/stefan/7916125/working/building/REAL250005043834 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043834

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043834/0 /scratch/stefan/7916125/working/building/REAL250005043834 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/951
`/scratch/stefan/7916125/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043834 none CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 12, 1, 1, 1, 1] 12
rigid atoms, others: [32, 34, 35, 4, 37, 6, 7, 8, 9, 10, 18, 19, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 28
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043834 none CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 12, 12, 12, 12] 12
rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 25
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043834 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043834
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043834/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043834
Building REAL250005043835
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043835'
/scratch/stefan/7916125/working/building/REAL250005043835 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043835

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043835/0 /scratch/stefan/7916125/working/building/REAL250005043835 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/952
`/scratch/stefan/7916125/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043835 none C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [66, 27, 66, 20, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 66, 66, 66, 66, 66, 27, 27, 20, 20, 1, 1, 1, 1, 33, 1, 1, 1, 1] 141
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 271
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043835 none C=C(C)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
141  conformations in input
total number of sets (complete confs): 141
using faster count positions algorithm for large data
unique positions, atoms: [141, 141, 141, 136, 91, 33, 91, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 141, 141, 141, 141, 141, 141, 141, 136, 136, 33, 33, 33, 33, 1, 33, 33, 33, 33] 141
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 473
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043835 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043835
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043835/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043835
Building REAL250005043836
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043836'
/scratch/stefan/7916125/working/building/REAL250005043836 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043836

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043836/0 /scratch/stefan/7916125/working/building/REAL250005043836 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/953
`/scratch/stefan/7916125/working/3D/953' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1)

`REAL250005043836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043836 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 64, 64, 73, 90, 73, 73, 23, 23, 1, 23, 23, 23, 23, 90, 90, 73, 73, 73, 73, 23, 23, 23, 23] 90
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 290
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043836 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 7, 7, 10, 34, 10, 10, 1, 1, 23, 1, 1, 1, 1, 34, 34, 10, 10, 10, 10, 1, 1, 1, 1] 90
rigid atoms, others: [32, 1, 34, 35, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 153
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: REAL250005043836 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(CF)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 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
90  conformations in input
total number of sets (complete confs): 90
using faster count positions algorithm for large data
unique positions, atoms: [42, 10, 42, 73, 73, 73, 73, 73, 10, 10, 10, 4, 1, 4, 1, 1, 10, 1, 1, 10, 10, 73, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 90
rigid atoms, others: [12, 14, 15, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35])
total number of confs: 183
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043836 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043836
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043836/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043836
Building REAL250005043837
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043837'
/scratch/stefan/7916125/working/building/REAL250005043837 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043837

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043837/0 /scratch/stefan/7916125/working/building/REAL250005043837 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/954
`/scratch/stefan/7916125/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043837 none CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 16, 31, 7, 16, 1, 7, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 1, 1, 1, 1, 31, 1, 1, 1, 1] 109
rigid atoms, others: [32, 33, 34, 35, 5, 38, 7, 8, 9, 10, 11, 40, 19, 20, 39, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 179
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043837 none CC(C)C(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 104, 109, 86, 104, 31, 86, 31, 31, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 31, 31, 109, 109, 109, 109, 109, 109, 109, 104, 104, 104, 104, 31, 31, 31, 31, 1, 31, 31, 31, 31] 109
rigid atoms, others: [36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 340
number of broken/clashed sets: 59
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043837 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043837
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043837/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043837
Building REAL250005043838
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043838'
/scratch/stefan/7916125/working/building/REAL250005043838 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043838

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043838/0 /scratch/stefan/7916125/working/building/REAL250005043838 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/955
`/scratch/stefan/7916125/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043838 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 30, 30, 30, 30, 108, 108, 186, 186, 186, 186, 186, 30, 30, 3, 3, 3, 3, 3, 1, 1, 30, 30, 30, 30, 186, 30, 30, 30, 30] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 28, 29] set([0, 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])
total number of confs: 385
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043838 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 30, 30, 30, 30, 6, 30, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 49, 49, 49, 49, 49, 30, 30, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 236
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: REAL250005043838 none CC[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 186, 186, 186, 115, 186, 36, 115, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 186, 186, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [34, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 618
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043838 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043838
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043838/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043838
Building REAL250005043839
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043839'
/scratch/stefan/7916125/working/building/REAL250005043839 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043839

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043839/0 /scratch/stefan/7916125/working/building/REAL250005043839 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/956
`/scratch/stefan/7916125/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1)

`REAL250005043839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043839 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 30, 30, 30, 73, 73, 107, 107, 107, 107, 30, 30, 1, 30, 30, 30, 30, 107, 107, 107, 107, 107, 107, 107, 30, 30, 30, 30] 107
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 305
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043839 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 6, 26, 26, 26, 26, 1, 1, 30, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1] 107
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 108
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: REAL250005043839 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CC23CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [87, 26, 87, 107, 107, 107, 107, 107, 26, 26, 25, 9, 1, 9, 1, 1, 1, 1, 1, 26, 26, 107, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 107
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 251
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043839 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043839
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043839/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043839
Building REAL250005043840
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043840'
/scratch/stefan/7916125/working/building/REAL250005043840 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043840

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043840/0 /scratch/stefan/7916125/working/building/REAL250005043840 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/957
`/scratch/stefan/7916125/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1)

`REAL250005043840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043840 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 84, 84, 102, 102, 102, 102, 102, 33, 33, 1, 33, 33, 33, 33, 102, 102, 102, 102, 102, 102, 33, 33, 33, 33] 102
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 267
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043840 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 1, 1, 33, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 102
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 20, 21, 23, 24, 25, 26] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 22, 27, 28, 29, 30, 31])
total number of confs: 105
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: REAL250005043840 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
102  conformations in input
total number of sets (complete confs): 102
using faster count positions algorithm for large data
unique positions, atoms: [76, 23, 76, 102, 102, 102, 102, 102, 23, 23, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 102, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23] 102
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36])
total number of confs: 233
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043840 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043840
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043840/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043840
Building REAL250005043841
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043841'
/scratch/stefan/7916125/working/building/REAL250005043841 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043841

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043841/0 /scratch/stefan/7916125/working/building/REAL250005043841 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/958
`/scratch/stefan/7916125/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043841 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 28, 28, 60, 60, 60, 60, 176, 176, 201, 201, 201, 201, 201, 60, 60, 1, 1, 2, 2, 2, 7, 7, 60, 60, 60, 60, 201, 60, 60, 60, 60, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 493
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043841 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 60, 60, 60, 60, 60, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1, 60, 60, 60, 60] 201
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38])
total number of confs: 238
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: REAL250005043841 none CC1(CC(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 105, 33, 105, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 201, 201, 201, 201, 201, 156, 156, 33, 33, 33, 33, 1, 33, 33, 33, 33, 201, 201, 201, 201] 201
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 678
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043841 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043841
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043841/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043841
Building REAL250005043842
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043842'
/scratch/stefan/7916125/working/building/REAL250005043842 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043842

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043842/0 /scratch/stefan/7916125/working/building/REAL250005043842 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/959
`/scratch/stefan/7916125/working/3D/959' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043842 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 9, 9, 9, 9, 39, 39, 56, 56, 56, 56, 56, 9, 9, 1, 1, 2, 2, 2, 9, 9, 9, 9, 56, 9, 9, 9, 9, 1, 1, 1, 1] 56
rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 127
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043842 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 16, 1, 1, 1, 1, 9, 9, 9, 9] 56
rigid atoms, others: [2, 4, 5, 6, 7, 8, 16, 17, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 1, 34, 3, 33, 35, 32, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 27])
total number of confs: 51
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: REAL250005043842 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 16, 43, 16, 16, 16, 10, 1, 10, 1, 1, 1, 1, 1, 1, 16, 16, 56, 56, 56, 56, 56, 16, 16, 16, 16, 1, 16, 16, 16, 16, 56, 56, 56, 56] 56
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 160
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043842 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043842
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043842/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043842
Building REAL250005043843
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043843'
/scratch/stefan/7916125/working/building/REAL250005043843 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043843

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043843/0 /scratch/stefan/7916125/working/building/REAL250005043843 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/960
`/scratch/stefan/7916125/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043843 none O=C(C1=CNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [11, 1, 1, 1, 1, 1, 1, 11, 32, 32, 32, 32, 88, 89, 125, 125, 125, 125, 125, 32, 32, 1, 1, 1, 1, 32, 32, 32, 32, 125, 32, 32, 32, 32] 125
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 285
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043843 none O=C(C1=CNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 32, 32, 32, 32, 1, 1, 1, 1, 33, 1, 1, 1, 1] 125
rigid atoms, others: [32, 1, 33, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 92
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043843 none O=C(C1=CNC=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [78, 33, 78, 125, 125, 125, 125, 33, 33, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 125, 125, 125, 125, 33, 33, 33, 33, 1, 33, 33, 33, 33] 125
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 280
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043843 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043843
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043843/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043843
Building REAL250005043844
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043844'
/scratch/stefan/7916125/working/building/REAL250005043844 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043844

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043844/0 /scratch/stefan/7916125/working/building/REAL250005043844 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/961
`/scratch/stefan/7916125/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043844 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 93, 93, 111, 111, 111, 111, 111, 33, 33, 1, 1, 33, 33, 33, 33, 111, 33, 33, 33, 33] 111
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 267
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043844 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 33, 33, 1, 1, 1, 1, 33, 1, 1, 1, 1] 111
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 93
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043844 none O=C(C1=CN=CO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [81, 33, 81, 111, 111, 111, 111, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 111, 111, 33, 33, 33, 33, 1, 33, 33, 33, 33] 111
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 249
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043844 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043844
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043844/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043844
Building REAL250005043845
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043845'
/scratch/stefan/7916125/working/building/REAL250005043845 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043845

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043845/0 /scratch/stefan/7916125/working/building/REAL250005043845 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/962
`/scratch/stefan/7916125/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043845 none C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [13, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 29, 29, 29, 29, 29, 1, 1, 13, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 29, 1, 1, 1, 1] 54
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 77
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043845 none C=CC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 52, 54, 54, 25, 54, 29, 29, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 29, 29, 54, 54, 54, 54, 54, 54, 54, 54, 54, 29, 29, 29, 29, 1, 29, 29, 29, 29] 54
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 160
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043845 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043845
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043845/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043845
Building REAL250005043846
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043846'
/scratch/stefan/7916125/working/building/REAL250005043846 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043846

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043846/0 /scratch/stefan/7916125/working/building/REAL250005043846 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/963
`/scratch/stefan/7916125/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043846 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 78, 78, 96, 96, 96, 96, 96, 24, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 96, 24, 24, 24, 24] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043846 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 31])
total number of confs: 105
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: REAL250005043846 none C[C@@H]1C[C@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 73, 96, 31, 73, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 96, 96, 96, 96, 96, 31, 31, 31, 31, 1, 31, 31, 31, 31] 96
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 271
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043846 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043846
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043846/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043846
Building REAL250005043847
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043847'
/scratch/stefan/7916125/working/building/REAL250005043847 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043847

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043847/0 /scratch/stefan/7916125/working/building/REAL250005043847 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/964
`/scratch/stefan/7916125/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1)

`REAL250005043847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043847 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 3, 3, 5, 5, 5, 5, 21, 21, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 27, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 27
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 34, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 68
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043847 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 27
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 16, 17, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 28, 33, 34, 35, 36, 37, 38])
total number of confs: 34
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: REAL250005043847 none CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [27, 23, 11, 23, 11, 11, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 27, 27, 27, 27, 27, 27, 11, 11, 11, 11, 1, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27] 27
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 84
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043847 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043847
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043847/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043847
Building REAL250005043848
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043848'
/scratch/stefan/7916125/working/building/REAL250005043848 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043848

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043848/0 /scratch/stefan/7916125/working/building/REAL250005043848 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/965
`/scratch/stefan/7916125/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043848 none CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 36, 36, 36, 36, 36, 22, 1, 1, 1, 1, 28, 1, 1, 1, 1] 130
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 210
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043848 none CCC(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 126, 81, 126, 28, 81, 28, 28, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 28, 130, 130, 130, 130, 130, 126, 28, 28, 28, 28, 1, 28, 28, 28, 28] 130
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 450
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043848 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043848
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043848/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043848
Building REAL250005043849
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043849'
/scratch/stefan/7916125/working/building/REAL250005043849 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043849

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043849/0 /scratch/stefan/7916125/working/building/REAL250005043849 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/966
`/scratch/stefan/7916125/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043849 none O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 30, 58, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 22, 22, 34, 34, 56, 56, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 317
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043849 none O=C(CCCF)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 95, 151, 201, 201, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 151, 151, 201, 201, 201, 201, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 799
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043849 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043849
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043849/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043849
Building REAL250005043850
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043850'
/scratch/stefan/7916125/working/building/REAL250005043850 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043850

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043850/0 /scratch/stefan/7916125/working/building/REAL250005043850 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/967
`/scratch/stefan/7916125/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043850 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 78, 78, 96, 96, 96, 96, 96, 24, 24, 2, 2, 2, 1, 1, 24, 24, 24, 24, 96, 24, 24, 24, 24] 96
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 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, 33, 34, 35])
total number of confs: 225
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043850 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 24, 24, 24, 24, 24, 1, 1, 1, 1, 31, 1, 1, 1, 1] 96
rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 20, 21, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 31])
total number of confs: 105
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: REAL250005043850 none C[C@H]1C[C@@H]1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
96  conformations in input
total number of sets (complete confs): 96
using faster count positions algorithm for large data
unique positions, atoms: [96, 96, 96, 96, 73, 96, 31, 73, 31, 31, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 96, 96, 96, 96, 96, 31, 31, 31, 31, 1, 31, 31, 31, 31] 96
rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 286
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043850 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043850
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043850/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043850
Building REAL250005043851
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043851'
/scratch/stefan/7916125/working/building/REAL250005043851 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043851

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043851/0 /scratch/stefan/7916125/working/building/REAL250005043851 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/968
`/scratch/stefan/7916125/working/3D/968' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043851 none CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [26, 17, 26, 7, 17, 1, 7, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 26, 26, 26, 26, 26, 26, 26, 17, 1, 1, 1, 1, 34, 1, 1, 1, 1] 116
rigid atoms, others: [32, 34, 35, 36, 5, 7, 8, 9, 10, 11, 37, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 33])
total number of confs: 158
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043851 none CC(C)C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
116  conformations in input
total number of sets (complete confs): 116
using faster count positions algorithm for large data
unique positions, atoms: [116, 98, 116, 82, 98, 34, 82, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 116, 116, 116, 116, 116, 116, 116, 98, 34, 34, 34, 34, 1, 34, 34, 34, 34] 116
rigid atoms, others: [33, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37])
total number of confs: 389
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043851 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043851
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043851/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043851
Building REAL250005043852
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043852'
/scratch/stefan/7916125/working/building/REAL250005043852 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043852

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043852/0 /scratch/stefan/7916125/working/building/REAL250005043852 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/969
`/scratch/stefan/7916125/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043852 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 91, 91, 113, 113, 113, 113, 113, 33, 33, 1, 1, 33, 33, 33, 33, 113, 33, 33, 33, 33] 113
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31])
total number of confs: 261
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043852 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 33, 33, 1, 1, 1, 1, 34, 1, 1, 1, 1] 113
rigid atoms, others: [1, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 27])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043852 none O=C(C1=NNN=C1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
113  conformations in input
total number of sets (complete confs): 113
using faster count positions algorithm for large data
unique positions, atoms: [87, 34, 87, 113, 113, 113, 113, 34, 34, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 113, 113, 34, 34, 34, 34, 1, 34, 34, 34, 34] 113
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31])
total number of confs: 271
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043852 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043852
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043852/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043852
Building REAL250005043853
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043853'
/scratch/stefan/7916125/working/building/REAL250005043853 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043853

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043853/0 /scratch/stefan/7916125/working/building/REAL250005043853 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/970
`/scratch/stefan/7916125/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043853 none O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 21, 21, 63, 1, 1, 1, 1, 34, 1, 1, 1, 1] 255
rigid atoms, others: [1, 4, 5, 6, 7, 8, 16, 17, 21, 22, 23, 24, 26, 27, 28, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 25])
total number of confs: 186
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043853 none O=C(CO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
255  conformations in input
total number of sets (complete confs): 255
using faster count positions algorithm for large data
unique positions, atoms: [64, 34, 64, 85, 34, 34, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 85, 85, 255, 34, 34, 34, 34, 1, 34, 34, 34, 34] 255
rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29])
total number of confs: 544
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043853 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043853
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043853/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043853
Building REAL250005043854
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043854'
/scratch/stefan/7916125/working/building/REAL250005043854 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043854

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043854/0 /scratch/stefan/7916125/working/building/REAL250005043854 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/971
`/scratch/stefan/7916125/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043854 none NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 94, 35, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 94, 94, 35, 35, 1, 1, 1, 1, 28, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 294
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043854 none NC(=O)C=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 185, 201, 185, 99, 28, 99, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 185, 185, 28, 28, 28, 28, 1, 28, 28, 28, 28] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 596
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043854 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043854
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043854/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043854
Building REAL250005043855
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043855'
/scratch/stefan/7916125/working/building/REAL250005043855 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043855

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043855/0 /scratch/stefan/7916125/working/building/REAL250005043855 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/972
`/scratch/stefan/7916125/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043855 none COC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 98, 29, 98, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 98, 98, 98, 29, 29, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 316
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043855 none COC(=O)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 201, 55, 17, 55, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 201, 132, 132, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 739
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043855 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043855
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043855/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043855
Building REAL250005043856
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043856'
/scratch/stefan/7916125/working/building/REAL250005043856 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043856

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043856/0 /scratch/stefan/7916125/working/building/REAL250005043856 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/973
`/scratch/stefan/7916125/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043856 none CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [107, 30, 30, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 32, 1, 1, 107, 107, 107, 30, 30, 1, 1, 1, 1, 32, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 219
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043856 none CSC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 184, 184, 100, 32, 100, 32, 32, 32, 10, 1, 10, 1, 1, 1, 1, 1, 1, 32, 32, 201, 201, 201, 184, 184, 32, 32, 32, 32, 1, 32, 32, 32, 32] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 553
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043856 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043856
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043856/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043856
Building REAL250005043857
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043857'
/scratch/stefan/7916125/working/building/REAL250005043857 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043857

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043857/0 /scratch/stefan/7916125/working/building/REAL250005043857 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/974
`/scratch/stefan/7916125/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043857 none NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 87, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 1, 1, 88, 88, 32, 32, 24, 24, 1, 1, 1, 1, 19, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 319
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043857 none NC(=O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 135, 83, 19, 83, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 171, 171, 135, 135, 19, 19, 19, 19, 1, 19, 19, 19, 19] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 788
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043857 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043857
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043857/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043857
Building REAL250005043858
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043858'
/scratch/stefan/7916125/working/building/REAL250005043858 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043858

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043858/0 /scratch/stefan/7916125/working/building/REAL250005043858 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/975
`/scratch/stefan/7916125/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1)

`REAL250005043858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043858 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [11, 1, 1, 1, 1, 1, 1, 1, 11, 22, 22, 22, 20, 66, 67, 89, 89, 89, 22, 22, 1, 22, 22, 22, 22, 89, 89, 89, 89, 89, 22, 22, 22, 22] 89
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 261
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043858 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 1, 1, 22, 1, 1, 1, 1, 23, 23, 23, 23, 23, 1, 1, 1, 1] 89
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 94
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: REAL250005043858 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2CCO2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
89  conformations in input
total number of sets (complete confs): 89
using faster count positions algorithm for large data
unique positions, atoms: [76, 23, 76, 89, 89, 89, 89, 89, 23, 23, 23, 8, 1, 8, 1, 1, 1, 1, 23, 23, 89, 23, 23, 23, 23, 1, 1, 1, 1, 1, 23, 23, 23, 23] 89
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33])
total number of confs: 207
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043858 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043858
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043858/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043858
Building REAL250005043859
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043859'
/scratch/stefan/7916125/working/building/REAL250005043859 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043859

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043859/0 /scratch/stefan/7916125/working/building/REAL250005043859 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/976
`/scratch/stefan/7916125/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1)

`REAL250005043859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043859 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 24, 56, 56, 85, 85, 85, 24, 24, 1, 24, 24, 24, 24, 85, 85, 85, 85, 24, 24, 24, 24] 85
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 257
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043859 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 1, 1, 24, 1, 1, 1, 1, 15, 15, 15, 15, 1, 1, 1, 1] 85
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28])
total number of confs: 80
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043859 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(Cl)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [56, 15, 56, 85, 85, 85, 85, 85, 15, 15, 15, 7, 1, 7, 1, 1, 1, 1, 15, 15, 85, 15, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 85
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 193
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043859 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043859
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043859/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043859
Building REAL250005043860
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043860'
/scratch/stefan/7916125/working/building/REAL250005043860 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043860

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043860/0 /scratch/stefan/7916125/working/building/REAL250005043860 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/977
`/scratch/stefan/7916125/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043860 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 33, 102, 102, 131, 131, 131, 131, 131, 33, 33, 1, 1, 1, 1, 1, 33, 33, 33, 33, 131, 33, 33, 33, 33] 131
rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043860 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 33, 33, 33, 33, 1, 1, 1, 1, 1, 7, 7, 38, 38, 38, 38, 38, 1, 1, 33, 33, 33, 33, 33, 1, 1, 1, 1, 38, 1, 1, 1, 1] 131
rigid atoms, others: [32, 1, 34, 33, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043860 none O=C(C1=CCCO1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
131  conformations in input
total number of sets (complete confs): 131
using faster count positions algorithm for large data
unique positions, atoms: [100, 38, 100, 131, 131, 131, 131, 38, 38, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 38, 38, 131, 131, 131, 131, 131, 38, 38, 38, 38, 1, 38, 38, 38, 38] 131
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 289
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043860 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043860
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043860/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043860
Building REAL250005043861
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043861'
/scratch/stefan/7916125/working/building/REAL250005043861 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043861

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043861/0 /scratch/stefan/7916125/working/building/REAL250005043861 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/978
`/scratch/stefan/7916125/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1)

`REAL250005043861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043861 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 30, 30, 30, 30, 68, 68, 92, 92, 92, 30, 30, 1, 30, 30, 30, 30, 92, 92, 92, 92, 92, 30, 30, 30, 30] 92
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 266
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043861 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 1, 1, 30, 1, 1, 1, 1, 19, 19, 19, 19, 19, 1, 1, 1, 1] 92
rigid atoms, others: [32, 1, 33, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28, 29])
total number of confs: 94
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043861 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2COC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 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]
0  hydrogens need rotated
92  conformations in input
total number of sets (complete confs): 92
using faster count positions algorithm for large data
unique positions, atoms: [72, 19, 72, 92, 92, 92, 92, 92, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 19, 19, 92, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 19, 19] 92
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33])
total number of confs: 215
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043861 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043861
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043861/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043861
Building REAL250005043862
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043862'
/scratch/stefan/7916125/working/building/REAL250005043862 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043862

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043862/0 /scratch/stefan/7916125/working/building/REAL250005043862 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/979
`/scratch/stefan/7916125/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043862 none O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 30, 30, 98, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 30, 30, 98, 98, 294, 1, 1, 1, 1, 33, 1, 1, 1, 1] 603
rigid atoms, others: [32, 1, 33, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 2, 3, 4, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 677
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043862 none O=C(C=CCO)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [108, 33, 108, 181, 181, 201, 33, 33, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 33, 33, 181, 181, 201, 201, 603, 33, 33, 33, 33, 1, 33, 33, 33, 33] 603
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 1232
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043862 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043862
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043862/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043862
Building REAL250005043863
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043863'
/scratch/stefan/7916125/working/building/REAL250005043863 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043863

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043863/0 /scratch/stefan/7916125/working/building/REAL250005043863 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/980
`/scratch/stefan/7916125/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043863 none CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 70, 24, 6, 24, 1, 6, 1, 1, 1, 1, 1, 7, 7, 28, 28, 28, 28, 28, 1, 1, 70, 70, 70, 70, 70, 24, 72, 1, 1, 1, 1, 28, 1, 1, 1, 1] 603
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 328
number of broken/clashed sets: 166
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043863 none CC=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 177, 92, 177, 28, 92, 28, 28, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 28, 28, 201, 201, 201, 201, 201, 177, 531, 28, 28, 28, 28, 1, 28, 28, 28, 28] 603
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 1282
number of broken/clashed sets: 166
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043863 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043863
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043863/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043863
Building REAL250005043864
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043864'
/scratch/stefan/7916125/working/building/REAL250005043864 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL250005043864

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043864/0 /scratch/stefan/7916125/working/building/REAL250005043864 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/981
`/scratch/stefan/7916125/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C)

`REAL250005043864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043864 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 7, 12, 1, 7, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 16, 1, 1, 12, 15, 15, 15, 12, 12, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 39
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 17, 18, 26, 27, 28, 29, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 30, 35, 36, 37, 38, 39, 40])
total number of confs: 89
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043864 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [36, 33, 36, 16, 33, 16, 16, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 16, 36, 39, 39, 39, 36, 36, 36, 16, 16, 16, 16, 1, 16, 16, 16, 16, 39, 39, 39, 39, 39, 39] 39
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 117
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043864 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043864/1 /scratch/stefan/7916125/working/building/REAL250005043864 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/982
`/scratch/stefan/7916125/working/3D/982' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C)

`REAL250005043864.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043864/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043864 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 7, 7, 34, 34, 34, 34, 34, 1, 1, 19, 33, 33, 19, 19, 19, 1, 1, 1, 1, 34, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33] 112
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 17, 18, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 29, 34, 35, 36, 37, 38, 39])
total number of confs: 166
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043864 none C[C@@H](C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)N(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
112  conformations in input
total number of sets (complete confs): 112
using faster count positions algorithm for large data
unique positions, atoms: [111, 95, 111, 34, 95, 34, 34, 34, 12, 1, 12, 1, 1, 1, 1, 1, 1, 34, 34, 111, 112, 112, 111, 111, 111, 34, 34, 34, 34, 1, 34, 34, 34, 34, 112, 112, 112, 112, 112, 112] 112
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 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: 323
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043864 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043864
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043864/1.*
0: /scratch/stefan/7916125/working/building/REAL250005043864/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043864
Building REAL250005043865
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043865'
/scratch/stefan/7916125/working/building/REAL250005043865 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043865

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043865/0 /scratch/stefan/7916125/working/building/REAL250005043865 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/983
`/scratch/stefan/7916125/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043865 none CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 39, 7, 39, 1, 7, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 71, 71, 71, 71, 71, 39, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043865 none CCC=C(F)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 99, 163, 27, 99, 27, 27, 27, 10, 1, 10, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 163, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 675
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043865 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043865
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043865/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043865
Building REAL250005043866
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043866'
/scratch/stefan/7916125/working/building/REAL250005043866 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043866

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043866/0 /scratch/stefan/7916125/working/building/REAL250005043866 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/984
`/scratch/stefan/7916125/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043866 none CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 31, 31, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 59, 59, 59, 59, 59, 31, 31, 1, 1, 1, 1, 37, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 269
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043866 none CCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 177, 177, 120, 37, 120, 37, 37, 37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 177, 177, 37, 37, 37, 37, 1, 37, 37, 37, 37] 201
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 623
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043866 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043866
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043866/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043866
Building REAL250005043867
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043867'
/scratch/stefan/7916125/working/building/REAL250005043867 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043867

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043867/0 /scratch/stefan/7916125/working/building/REAL250005043867 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/985
`/scratch/stefan/7916125/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043867 none [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 16, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 26, 26, 16, 16, 1, 1, 1, 1, 25, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 19, 20, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 29])
total number of confs: 217
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043867 none [N-]=[N+]=NCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'N.1', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 125, 100, 81, 25, 81, 25, 25, 25, 10, 1, 10, 1, 1, 1, 1, 1, 1, 25, 25, 125, 125, 100, 100, 25, 25, 25, 25, 1, 25, 25, 25, 25] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 568
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043867 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043867
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043867/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043867
Building REAL250005043868
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043868'
/scratch/stefan/7916125/working/building/REAL250005043868 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043868

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043868/0 /scratch/stefan/7916125/working/building/REAL250005043868 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/986
`/scratch/stefan/7916125/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043868 none C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [101, 101, 53, 20, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 101, 101, 101, 20, 20, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 19, 20, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30])
total number of confs: 386
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043868 none C#CCOCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 140, 90, 45, 13, 45, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 90, 90, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34])
total number of confs: 738
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043868 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043868
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043868/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043868
Building REAL250005043869
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043869'
/scratch/stefan/7916125/working/building/REAL250005043869 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043869

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043869/0 /scratch/stefan/7916125/working/building/REAL250005043869 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/987
`/scratch/stefan/7916125/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043869 none CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 32, 70, 22, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 70, 70, 70, 70, 210, 33, 33, 22, 22, 1, 1, 1, 1, 22, 1, 1, 1, 1] 603
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 554
number of broken/clashed sets: 115
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043869 none CC(O)CCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 162, 201, 145, 90, 22, 90, 22, 22, 22, 10, 1, 10, 1, 1, 1, 1, 1, 1, 22, 22, 201, 201, 201, 201, 603, 163, 163, 145, 145, 22, 22, 22, 22, 1, 22, 22, 22, 22] 603
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 1406
number of broken/clashed sets: 115
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043869 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043869
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043869/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043869
Building REAL250005043870
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043870'
/scratch/stefan/7916125/working/building/REAL250005043870 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043870

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043870/0 /scratch/stefan/7916125/working/building/REAL250005043870 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/988
`/scratch/stefan/7916125/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043870 none C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [40, 40, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 40, 40, 40, 27, 27, 1, 1, 1, 1, 25, 1, 1, 1, 1] 164
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 204
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043870 none C#CCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
164  conformations in input
total number of sets (complete confs): 164
using faster count positions algorithm for large data
unique positions, atoms: [164, 164, 146, 87, 25, 87, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 164, 164, 164, 146, 146, 25, 25, 25, 25, 1, 25, 25, 25, 25] 164
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 619
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043870 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043870
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043870/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043870
Building REAL250005043871
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043871'
/scratch/stefan/7916125/working/building/REAL250005043871 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043871

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043871/0 /scratch/stefan/7916125/working/building/REAL250005043871 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/989
`/scratch/stefan/7916125/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043871 none CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 43, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 68, 68, 68, 68, 68, 43, 43, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 232
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043871 none CC=CC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 121, 36, 121, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 201, 201, 185, 185, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 584
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043871 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043871
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043871/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043871
Building REAL250005043872
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043872'
/scratch/stefan/7916125/working/building/REAL250005043872 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043872

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043872/0 /scratch/stefan/7916125/working/building/REAL250005043872 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/990
`/scratch/stefan/7916125/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043872 none COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 81, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 13, 13, 13, 13, 13, 1, 1, 121, 121, 121, 81, 81, 21, 21, 1, 1, 1, 1, 13, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 386
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043872 none COCC=CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 107, 107, 57, 13, 57, 13, 13, 13, 6, 1, 6, 1, 1, 1, 1, 1, 1, 13, 13, 201, 201, 201, 192, 192, 107, 107, 13, 13, 13, 13, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 734
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043872 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043872
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043872/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043872
Building REAL250005043873
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043873'
/scratch/stefan/7916125/working/building/REAL250005043873 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043873

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043873/0 /scratch/stefan/7916125/working/building/REAL250005043873 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/991
`/scratch/stefan/7916125/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043873 none CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
207  conformations in input
total number of sets (complete confs): 207
using faster count positions algorithm for large data
unique positions, atoms: [10, 6, 5, 6, 6, 1, 5, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 10, 10, 10, 10, 10, 6, 6, 6, 18, 1, 1, 1, 1, 25, 1, 1, 1, 1] 207
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 94
number of broken/clashed sets: 161
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043873 none CCC(C)(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
207  conformations in input
total number of sets (complete confs): 207
using faster count positions algorithm for large data
unique positions, atoms: [69, 58, 57, 58, 58, 25, 57, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 69, 69, 69, 69, 69, 58, 58, 58, 174, 25, 25, 25, 25, 1, 25, 25, 25, 25] 207
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 397
number of broken/clashed sets: 161
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043873 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043873
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043873/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043873
Building REAL250005043874
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043874'
/scratch/stefan/7916125/working/building/REAL250005043874 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043874

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043874/0 /scratch/stefan/7916125/working/building/REAL250005043874 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/992
`/scratch/stefan/7916125/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043874 none C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 52, 20, 7, 20, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 52, 52, 52, 20, 20, 20, 20, 1, 1, 1, 1, 36, 1, 1, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 265
number of broken/clashed sets: 102
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043874 none C#CCC(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 112, 158, 36, 112, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 201, 201, 201, 158, 158, 158, 158, 36, 36, 36, 36, 1, 36, 36, 36, 36] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 782
number of broken/clashed sets: 102
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043874 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043874
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043874/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043874
Building REAL250005043875
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043875'
/scratch/stefan/7916125/working/building/REAL250005043875 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043875

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043875/0 /scratch/stefan/7916125/working/building/REAL250005043875 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/993
`/scratch/stefan/7916125/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043875 none C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
510  conformations in input
total number of sets (complete confs): 510
using faster count positions algorithm for large data
unique positions, atoms: [63, 22, 6, 22, 1, 6, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 63, 63, 63, 22, 66, 1, 1, 1, 1, 33, 1, 1, 1, 1] 510
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 18, 19, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 29])
total number of confs: 309
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043875 none C=CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
510  conformations in input
total number of sets (complete confs): 510
using faster count positions algorithm for large data
unique positions, atoms: [170, 170, 106, 170, 33, 106, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 170, 170, 170, 170, 510, 33, 33, 33, 33, 1, 33, 33, 33, 33] 510
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33])
total number of confs: 1105
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043875 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043875
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043875/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043875
Building REAL250005043876
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043876'
/scratch/stefan/7916125/working/building/REAL250005043876 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043876

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043876/0 /scratch/stefan/7916125/working/building/REAL250005043876 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/994
`/scratch/stefan/7916125/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1)

`REAL250005043876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043876 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [10, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 54, 54, 67, 67, 67, 67, 25, 25, 1, 25, 25, 25, 25, 67, 67, 67, 67, 67, 67, 67, 25, 25, 25, 25] 67
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 154
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043876 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 6, 6, 13, 13, 13, 13, 1, 1, 25, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 67
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 63
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043876 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C23CC2CC3)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
67  conformations in input
total number of sets (complete confs): 67
using faster count positions algorithm for large data
unique positions, atoms: [51, 13, 51, 67, 67, 67, 67, 67, 13, 13, 13, 4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 67, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 67
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 148
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043876 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043876
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043876/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043876
Building REAL250005043877
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043877'
/scratch/stefan/7916125/working/building/REAL250005043877 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043877

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043877/0 /scratch/stefan/7916125/working/building/REAL250005043877 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/995
`/scratch/stefan/7916125/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043877 none C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [79, 58, 31, 58, 58, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 79, 79, 79, 58, 58, 58, 31, 31, 1, 1, 1, 1, 21, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 35, 36, 37, 6, 8, 9, 10, 11, 12, 20, 21, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 354
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043877 none C=C[C@H](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 158, 201, 201, 79, 21, 79, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 201, 201, 201, 201, 201, 201, 158, 158, 21, 21, 21, 21, 1, 21, 21, 21, 21] 201
rigid atoms, others: [34, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 806
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043877 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043877
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043877/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043877
Building REAL250005043878
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043878'
/scratch/stefan/7916125/working/building/REAL250005043878 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043878

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043878/0 /scratch/stefan/7916125/working/building/REAL250005043878 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/996
`/scratch/stefan/7916125/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043878 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 9, 9, 1, 1, 1, 1, 52, 92, 92, 92, 92, 184, 184, 201, 201, 201, 201, 201, 92, 92, 9, 9, 1, 1, 1, 1, 1, 92, 92, 92, 92, 201, 92, 92, 92, 92] 201
rigid atoms, others: [3, 4, 5, 6, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 484
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043878 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 30, 92, 92, 1, 1, 1, 1, 1, 7, 7, 22, 22, 22, 22, 22, 1, 1, 30, 30, 92, 92, 92, 92, 92, 1, 1, 1, 1, 22, 1, 1, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 33, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 276
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: REAL250005043878 none O=C(C=CC1CC1)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 92, 156, 156, 201, 201, 22, 22, 22, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 156, 156, 201, 201, 201, 201, 201, 22, 22, 22, 22, 1, 22, 22, 22, 22] 201
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 632
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043878 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043878
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043878/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043878
Building REAL250005043879
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043879'
/scratch/stefan/7916125/working/building/REAL250005043879 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043879

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043879/0 /scratch/stefan/7916125/working/building/REAL250005043879 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/997
`/scratch/stefan/7916125/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043879 none CCC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [35, 21, 6, 21, 21, 1, 6, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 1, 1, 40, 40, 40, 40, 40, 21, 1, 1, 1, 1, 37, 1, 1, 1, 1] 182
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 253
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043879 none CCC(C#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
182  conformations in input
total number of sets (complete confs): 182
using faster count positions algorithm for large data
unique positions, atoms: [179, 165, 118, 165, 165, 37, 118, 37, 37, 37, 10, 1, 10, 1, 1, 1, 1, 1, 1, 37, 37, 182, 182, 182, 182, 182, 165, 37, 37, 37, 37, 1, 37, 37, 37, 37] 182
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 655
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043879 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043879
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043879/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043879
Building REAL250005043880
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043880'
/scratch/stefan/7916125/working/building/REAL250005043880 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043880

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043880/0 /scratch/stefan/7916125/working/building/REAL250005043880 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/998
`/scratch/stefan/7916125/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1)

`REAL250005043880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043880 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 35, 35, 35, 35, 83, 83, 103, 103, 103, 103, 35, 34, 1, 35, 35, 35, 35, 103, 103, 103, 103, 103, 103, 103, 35, 35, 35, 35] 103
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 282
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043880 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 6, 6, 27, 27, 27, 27, 1, 1, 35, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1] 103
rigid atoms, others: [1, 34, 35, 36, 33, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25] set([0, 32, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 26, 27, 28, 29, 30, 31])
total number of confs: 115
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: REAL250005043880 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2C3CCC32)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 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, 3, 7, 3, 7, 7, 7, 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
103  conformations in input
total number of sets (complete confs): 103
using faster count positions algorithm for large data
unique positions, atoms: [81, 27, 81, 103, 103, 103, 103, 103, 27, 27, 27, 8, 1, 8, 1, 1, 1, 1, 1, 27, 27, 103, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 103
rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36])
total number of confs: 231
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043880 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043880
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043880/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043880
Building REAL250005043881
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043881'
/scratch/stefan/7916125/working/building/REAL250005043881 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043881

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043881/0 /scratch/stefan/7916125/working/building/REAL250005043881 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/999
`/scratch/stefan/7916125/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043881 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 24, 24, 24, 24, 81, 81, 105, 105, 105, 105, 105, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 105, 24, 24, 24, 24] 105
rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 240
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043881 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 36, 1, 1, 1, 1] 105
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 6, 32, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27])
total number of confs: 110
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: REAL250005043881 none C=C1CCC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
105  conformations in input
total number of sets (complete confs): 105
using faster count positions algorithm for large data
unique positions, atoms: [105, 105, 105, 105, 85, 36, 85, 36, 36, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 105, 105, 105, 105, 105, 105, 105, 36, 36, 36, 36, 1, 36, 36, 36, 36] 105
rigid atoms, others: [32, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36])
total number of confs: 287
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043881 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043881
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043881/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043881
Building REAL250005043882
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043882'
/scratch/stefan/7916125/working/building/REAL250005043882 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043882

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043882/0 /scratch/stefan/7916125/working/building/REAL250005043882 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1000
`/scratch/stefan/7916125/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C)

`REAL250005043882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043882 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 31, 31, 45, 45, 45, 45, 45, 7, 7, 1, 1, 1, 2, 2, 2, 1, 7, 7, 7, 7, 45, 7, 7, 7, 7, 2, 2, 2] 45
rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043882 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 26, 1, 1, 1, 1, 7, 7, 7] 45
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 31, 36, 37, 38])
total number of confs: 56
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043882 none C[C@H]1C(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)[C@H]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
45  conformations in input
total number of sets (complete confs): 45
using default count positions algorithm for smaller data
unique positions, atoms: [45, 45, 45, 42, 26, 42, 26, 26, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 26, 45, 45, 45, 45, 45, 45, 45, 26, 26, 26, 26, 1, 26, 26, 26, 26, 45, 45, 45] 45
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 113
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043882 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043882
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043882/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043882
Building REAL250005043883
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043883'
/scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL250005043883

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043883/0 /scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1001
`/scratch/stefan/7916125/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [22, 18, 8, 18, 18, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 22, 22, 22, 22, 22, 18, 18, 18, 8, 8, 1, 1, 1, 1, 21, 1, 1, 1, 1] 87
rigid atoms, others: [32, 33, 34, 35, 37, 6, 39, 8, 9, 10, 11, 12, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 125
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CC[N@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
87  conformations in input
total number of sets (complete confs): 87
using faster count positions algorithm for large data
unique positions, atoms: [87, 84, 59, 84, 84, 57, 21, 57, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 87, 87, 87, 87, 87, 84, 84, 84, 59, 59, 21, 21, 21, 21, 1, 21, 21, 21, 21] 87
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 312
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `1'
/scratch/stefan/7916125/working/building/REAL250005043883/1 /scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 1 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1002
`/scratch/stefan/7916125/working/3D/1002' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043883.mol2' -> `1.mol2'
`temp.mol2' -> `REAL250005043883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043883/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [21, 17, 8, 17, 17, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 1, 1, 21, 21, 21, 21, 21, 17, 17, 17, 8, 8, 1, 1, 1, 1, 21, 1, 1, 1, 1] 86
rigid atoms, others: [32, 33, 34, 35, 37, 6, 39, 8, 9, 10, 11, 12, 40, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36])
total number of confs: 122
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CC[N@@H+](C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 83, 58, 83, 83, 56, 21, 56, 21, 21, 21, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 86, 86, 86, 86, 86, 83, 83, 83, 58, 58, 21, 21, 21, 21, 1, 21, 21, 21, 21] 86
rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 310
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
mkdir: created directory `2'
/scratch/stefan/7916125/working/building/REAL250005043883/2 /scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 2 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1003
`/scratch/stefan/7916125/working/3D/1003' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043883.mol2' -> `2.mol2'
`temp.mol2' -> `REAL250005043883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043883/2/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`2.mol2' -> `2.mol2.original'
`output.mol2' -> `2.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 48, 27, 48, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 1, 1, 68, 68, 68, 68, 68, 48, 48, 48, 27, 27, 1, 1, 1, 1, 27, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35])
total number of confs: 319
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043883 none CCN(C)CC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 182, 195, 105, 27, 105, 27, 27, 27, 9, 1, 9, 1, 1, 1, 1, 1, 1, 27, 27, 201, 201, 201, 201, 201, 195, 195, 195, 182, 182, 27, 27, 27, 27, 1, 27, 27, 27, 27] 201
rigid atoms, others: [35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39])
total number of confs: 728
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043883 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043883
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
1: /scratch/stefan/7916125/working/building/REAL250005043883/1.*
2: /scratch/stefan/7916125/working/building/REAL250005043883/2.*
0: /scratch/stefan/7916125/working/building/REAL250005043883/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043883
Building REAL250005043884
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043884'
/scratch/stefan/7916125/working/building/REAL250005043884 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043884

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043884/0 /scratch/stefan/7916125/working/building/REAL250005043884 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1004
`/scratch/stefan/7916125/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043884 none CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [18, 7, 18, 1, 7, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 18, 18, 18, 18, 54, 1, 1, 1, 1, 25, 1, 1, 1, 1] 210
rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 17, 18, 24, 25, 26, 27, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 28])
total number of confs: 155
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043884 none CC(O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
210  conformations in input
total number of sets (complete confs): 210
using faster count positions algorithm for large data
unique positions, atoms: [70, 59, 70, 25, 59, 25, 25, 25, 12, 1, 12, 1, 1, 1, 1, 1, 1, 25, 25, 70, 70, 70, 70, 210, 25, 25, 25, 25, 1, 25, 25, 25, 25] 210
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32])
total number of confs: 419
number of broken/clashed sets: 78
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043884 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043884
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043884/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043884
Building REAL250005043885
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043885'
/scratch/stefan/7916125/working/building/REAL250005043885 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043885

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043885/0 /scratch/stefan/7916125/working/building/REAL250005043885 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1005
`/scratch/stefan/7916125/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043885 none CC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [27, 7, 27, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 27, 27, 27, 1, 1, 1, 1, 33, 1, 1, 1, 1] 85
rigid atoms, others: [3, 5, 6, 7, 8, 9, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 26])
total number of confs: 113
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043885 none CC(=O)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 69, 85, 33, 69, 33, 33, 33, 12, 1, 12, 1, 1, 1, 1, 1, 1, 33, 33, 85, 85, 85, 33, 33, 33, 33, 1, 33, 33, 33, 33] 85
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30])
total number of confs: 225
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043885 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043885
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043885/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043885
Building REAL250005043886
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043886'
/scratch/stefan/7916125/working/building/REAL250005043886 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043886

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043886/0 /scratch/stefan/7916125/working/building/REAL250005043886 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1006
`/scratch/stefan/7916125/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043886 none N#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 20, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 17, 17, 1, 1, 55, 55, 32, 32, 20, 20, 1, 1, 1, 1, 17, 1, 1, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 315
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043886 none N#CCCCC(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 102, 59, 17, 59, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 201, 201, 130, 130, 102, 102, 17, 17, 17, 17, 1, 17, 17, 17, 17] 201
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 886
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043886 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043886
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043886/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043886
Building REAL250005043887
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043887'
/scratch/stefan/7916125/working/building/REAL250005043887 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043887

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043887/0 /scratch/stefan/7916125/working/building/REAL250005043887 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1007
`/scratch/stefan/7916125/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1)

`REAL250005043887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043887 none N#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 57, 57, 85, 85, 85, 85, 85, 11, 11, 1, 1, 11, 11, 11, 11, 85, 11, 11, 11, 11, 1, 1, 1, 1] 85
rigid atoms, others: [0, 1, 2, 3, 33, 32, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29])
total number of confs: 187
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043887 none N#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 33, 33, 33, 33, 33, 1, 1, 11, 11, 1, 1, 1, 1, 33, 1, 1, 1, 1, 11, 11, 11, 11] 85
rigid atoms, others: [3, 5, 6, 7, 8, 9, 17, 18, 21, 22, 23, 24, 26, 27, 28, 29] set([0, 1, 2, 4, 33, 32, 10, 11, 12, 13, 14, 15, 16, 19, 20, 25, 30, 31])
total number of confs: 77
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043887 none N#CC1(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)CC1 NO_LONG_NAME
dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [85, 85, 77, 33, 77, 33, 33, 33, 11, 1, 11, 1, 1, 1, 1, 1, 1, 33, 33, 85, 85, 33, 33, 33, 33, 1, 33, 33, 33, 33, 85, 85, 85, 85] 85
rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33])
total number of confs: 205
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043887 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043887
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043887/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043887
Building REAL250005043888
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043888'
/scratch/stefan/7916125/working/building/REAL250005043888 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043888

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043888/0 /scratch/stefan/7916125/working/building/REAL250005043888 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1008
`/scratch/stefan/7916125/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1)

`REAL250005043888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043888 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 8, 27, 27, 27, 27, 77, 77, 97, 97, 97, 97, 97, 27, 27, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 97, 27, 27, 27, 27, 1, 1] 97
rigid atoms, others: [0, 1, 2, 3, 4, 35, 20, 21, 22, 23, 24, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34])
total number of confs: 219
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043888 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 31, 31, 31, 31, 31, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 31, 1, 1, 1, 1, 27, 27] 97
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 18, 19, 26, 27, 28, 29, 31] set([0, 1, 2, 3, 36, 5, 11, 12, 13, 14, 15, 16, 17, 35, 20, 21, 22, 23, 24, 25, 30])
total number of confs: 111
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: REAL250005043888 none C=C1CC(C(=O)N2CCN(C(=O)C3=CC(=O)[N-]O3)CC2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 31, 81, 31, 31, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 31, 31, 97, 97, 97, 97, 97, 97, 31, 31, 31, 31, 1, 31, 31, 31, 31, 97, 97] 97
rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36])
total number of confs: 265
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043888 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043888
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043888/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043888
Building REAL250005043889
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043889'
/scratch/stefan/7916125/working/building/REAL250005043889 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043889

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043889/0 /scratch/stefan/7916125/working/building/REAL250005043889 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1009
`/scratch/stefan/7916125/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1)

`REAL250005043889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043889 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 1, 12, 30, 32, 32, 32, 64, 64, 83, 83, 83, 32, 32, 1, 32, 32, 32, 32, 83, 83, 83, 83, 32, 32, 32, 32] 83
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
total number of confs: 236
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043889 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 1, 1, 32, 1, 1, 1, 1, 20, 20, 20, 20, 1, 1, 1, 1] 83
rigid atoms, others: [32, 1, 8, 9, 10, 11, 12, 18, 19, 21, 22, 23, 24, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 25, 26, 27, 28])
total number of confs: 98
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043889 none O=C(C1=CC(=O)[N-]O1)N1CCN(C(=O)C2(F)CC2)CC1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 1, 1, 1, 11, 8, 12, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 3, 7, 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
83  conformations in input
total number of sets (complete confs): 83
using faster count positions algorithm for large data
unique positions, atoms: [65, 20, 65, 83, 83, 83, 83, 83, 20, 20, 20, 9, 1, 9, 1, 1, 1, 1, 20, 20, 83, 20, 20, 20, 20, 1, 1, 1, 1, 20, 20, 20, 20] 83
rigid atoms, others: [12, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32])
total number of confs: 193
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043889 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043889
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043889/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043889
Building REAL250005043890
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043890'
/scratch/stefan/7916125/working/building/REAL250005043890 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043890

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043890/0 /scratch/stefan/7916125/working/building/REAL250005043890 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1010
`/scratch/stefan/7916125/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043890 none COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [23, 9, 5, 9, 9, 1, 5, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 35, 1, 1, 23, 23, 23, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 35, 1, 1, 1, 1] 145
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 103
number of broken/clashed sets: 86
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043890 none COC(C)(C)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
145  conformations in input
total number of sets (complete confs): 145
using faster count positions algorithm for large data
unique positions, atoms: [145, 145, 99, 145, 145, 35, 99, 35, 35, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 35, 145, 145, 145, 145, 145, 145, 145, 145, 145, 35, 35, 35, 35, 1, 35, 35, 35, 35] 145
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 517
number of broken/clashed sets: 86
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043890 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043890
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043890/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043890
Building REAL250005043891
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043891'
/scratch/stefan/7916125/working/building/REAL250005043891 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043891

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043891/0 /scratch/stefan/7916125/working/building/REAL250005043891 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1011
`/scratch/stefan/7916125/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043891 none CC(CC#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [19, 7, 19, 51, 51, 1, 7, 1, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 36, 1, 1, 19, 19, 19, 19, 51, 51, 1, 1, 1, 1, 36, 1, 1, 1, 1] 197
rigid atoms, others: [32, 33, 34, 35, 5, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 31])
total number of confs: 259
number of broken/clashed sets: 101
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043891 none CC(CC#N)C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
197  conformations in input
total number of sets (complete confs): 197
using faster count positions algorithm for large data
unique positions, atoms: [145, 111, 145, 197, 197, 36, 111, 36, 36, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 36, 36, 145, 145, 145, 145, 197, 197, 36, 36, 36, 36, 1, 36, 36, 36, 36] 197
rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35])
total number of confs: 761
number of broken/clashed sets: 101
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043891 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043891
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043891/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043891
Building REAL250005043892
mkdir: created directory `/scratch/stefan/7916125/working/building/REAL250005043892'
/scratch/stefan/7916125/working/building/REAL250005043892 /scratch/stefan/7916125/working /scratch/stefan/7916125
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL250005043892

mkdir: created directory `0'
/scratch/stefan/7916125/working/building/REAL250005043892/0 /scratch/stefan/7916125/working/building/REAL250005043892 /scratch/stefan/7916125/working /scratch/stefan/7916125
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7916125/working/3D/1012
`/scratch/stefan/7916125/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1)

`REAL250005043892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL250005043892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7916125/working/building/REAL250005043892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043892 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
91  conformations in input
total number of sets (complete confs): 91
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 74, 74, 91, 91, 91, 91, 91, 25, 25, 2, 2, 2, 2, 2, 1, 1, 1, 1, 25, 25, 25, 25, 91, 25, 25, 25, 25] 91
rigid atoms, others: [1, 2, 3, 4, 5, 26, 27, 28, 29] set([0, 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])
total number of confs: 211
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL250005043892 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 6, 1, 6, 1, 1, 1, 1, 1, 7, 7, 25, 25, 25, 25, 25, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 25, 1, 1, 1, 1] 91
rigid atoms, others: [32, 33, 35, 36, 5, 38, 7, 8, 9, 10, 11, 19, 20, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34])
total number of confs: 101
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: REAL250005043892 none CCC1CC1C(=O)N1CCN(C(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 25, 73, 25, 25, 25, 11, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 91, 91, 91, 91, 91, 91, 91, 91, 91, 25, 25, 25, 25, 1, 25, 25, 25, 25] 91
rigid atoms, others: [34, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38])
total number of confs: 250
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7916125/working/building/REAL250005043892 /scratch/stefan/7916125/working /scratch/stefan/7916125

Finished preparing REAL250005043892
Recording results
/scratch/stefan/7916125/working /scratch/stefan/7916125
Appending to /scratch/stefan/7916125/finished/xaaaaaf.*
0: /scratch/stefan/7916125/working/building/REAL250005043892/0.*
Removing working files in /scratch/stefan/7916125/working/building/REAL250005043892
/scratch/stefan/7916125
Compressing combined databse files
/scratch/stefan/7916125/finished/xaaaaaf.db2.gz
/scratch/stefan/7916125/finished/xaaaaaf.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7916125/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7916125/working/3D/1013'
removed directory: `/scratch/stefan/7916125/working/3D'
`/scratch/stefan/7916125/working/protonate' -> `/scratch/stefan/7916125/archive'
`/scratch/stefan/7916125/working/input-smiles.ism' -> `/scratch/stefan/7916125/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7916125/working/building'
rmdir: removing directory, `/scratch/stefan/7916125/working'
ls: No match.
ls: No match.